EFFECTIVE POPULATION SIZE AND GENETIC DRIFT IN TRISTYLOUS EICHHORNIA PANICULATA (PONTEDERIACEAE)

Populations of the tristylous, annual Eichhornia paniculata are markedly differentiated with respect to frequency of mating types. This variation is associated with evolutionary changes in mating system, from predominant outcrossing to high self-fertilization. To assess the potential influence of genetic drift acting on this variation, we estimated effective population size in 10 populations from northeastern Brazil using genetic and demographic methods. Effective size (N_e) was inferred from temporal changes in allele frequency at two to eight isozyme loci and also calculated using five demographic variables: 1) the number of flowering individuals (N); 2) temporal fluctuations in N; 3) variance in flower number; 4) frequency of mating types; and 5) selfing rate. Average N_e based on isozyme data was 15.8, range 3.4–70.6, and represented a fraction (mean N_e/N = 0.106) of the census number of individuals (mean N = 762.8; range: 30.5–5,040). Temporal variation in N and variance in flower number each reduced N_e to about a half of N whereas mating type frequencies and selfing rate caused only small reductions in N_e relative to N. All estimates of N_e based on demographic variables were considerably larger than those obtained from genetic data. The two kinds of estimates were in general agreement, however, when all demographic variables were combined into a single measure. Monte Carlo simulations indicated that effective size must be fewer than about 40 for drift to overcome the frequency-dependent selection that maintains the polymorphism for mating type. Applying the average N_e/N value to 167 populations censused in northeastern Brazil indicated that 72% had effective sizes below this number. This suggests that genetic drift is likely to play a dominant role in natural populations of E. paniculata.     

A TEST AND REVIEW OF THE ROLE OF EFFECTIVE POPULATION SIZE ON EXPERIMENTAL SEXUAL SELECTION PATTERNS

Experimental evolution, particularly experimental sexual selection in which sexual selection strength is manipulated by altering the mating system, is an increasingly popular method for testing evolutionary theory. Concerns have arisen regarding genetic diversity variation across experimental treatments: differences in the number and sex ratio of breeders (effective population size; N_e ) and the potential for genetic hitchhiking, both of which may cause different levels of genetic variation between treatments. Such differences may affect the selection response and confound interpretation of results. Here we use both census-based estimators and molecular marker-based estimates to empirically test how experimental evolution of sexual selection in Drosophila pseudoobscura impacts N_e and autosomal genetic diversity. We also consider effects of treatment on X-linked N_e s, which have previously been ignored. Molecular autosomal marker-based estimators indicate that neither N_e nor genetic diversity differs between treatments experiencing different sexual selection intensities; thus observed evolutionary responses reflect selection rather than any confounding effects of experimental design. Given the increasing number of studies on experimental sexual selection, we also review the census N_e s of other experimental systems, calculate X-linked N_e , and compare how different studies have dealt with the issues of inbreeding, genetic drift, and genetic hitchhiking to help inform future designs.     

亚东鲑幼鱼饲料中适宜淀粉种类与水平的研究

为考察淀粉种类与水平对亚东鲑(Salmo trutta)幼鱼生长性能、饲料利用、消化酶活性、肝脏生化指标和组织学的影响, 实验采用2×3双因素设计, 选取玉米淀粉和木薯淀粉, 分别以5%、10%和15%水平添加, 共配制6种等氮等脂饲料, 饲喂初始体重为(0.50±0.03) g的亚东鲑幼鱼84d。结果表明, 随着饲料中玉米淀粉和木薯淀粉水平的提高, 增重率呈现先上升后下降的趋势, 饲料系数则先下降后上升(P<0.05), 其中10%木薯淀粉组增重率最高(518.8%), 饲料系数最低(1.32)。各组成活率、脏体比、肥满度和全鱼水分、粗蛋白质、粗脂肪和粗灰分含量均没有显著差异(P>0.05), 粗蛋白沉积率随淀粉水平的提高呈下降趋势, 其中15%水平组显著低于其他水平组(P<0.05), 而脂肪沉积率则随着淀粉水平的升高先上升后下降, 且10%木薯淀粉组显著高于玉米淀粉组(P<0.05); 淀粉种类和水平对胃蛋白酶和胃淀粉酶无显著影响(P>0.05), 15%淀粉水平组肠淀粉酶和肠蛋白酶活性显著高于其他水平组(P<0.05)。饲料中淀粉种类和水平对肝脏谷丙转氨酶、谷草转氨酶、总胆固醇和甘油三酯均无显著影响(P>0.05), 15%淀粉组的肝糖原含量显著高于其他水平组(P<0.05)。在肝脏组织学方面, 15%水平组较其余两个水平组表现出明显的细胞核移位和细胞空泡化现象。上述结果表明, 在实验条件下, 亚东鲑幼鱼饲料中淀粉的适宜添加水平为10%, 木薯淀粉的效果优于玉米淀粉。     

GENOME SIZE IS NOT CORRELATED WITH EFFECTIVE POPULATION SIZE IN THE ORYZA SPECIES

Genome sizes vary widely across the tree of life and the evolutionary mechanism underlined remains largely unknown. Lynch and Conery (2003) proposed that evolution of genome complexity was driven mainly by nonadaptive stochastic forces and presented the observation that genome size was negatively correlated with effective population size (N_e) as a strong support for their hypothesis. Here, we analyzed the relation between N_e and genome size for 10 diploid Oryza species that showed about fourfold genome size variation. Using sequences of more than 20 nuclear genes, we estimated N_e for each species after correction for the effects of demography and heterogeneity of mutation rates among loci and species. Pairwise comparisons and correlation analyses did not detect a negative relationship between N_e and genome size despite about 6.5‐fold interspecies N_e variation. By calculating phylogenetically independent contrasts (PICs) for N_e, we repeated correlation analysis and did not find any correlation between N_e and genome size. These observations suggest that the genome size variation in the Oryza species cannot be explained simply by the effect of effective population size.     

INCREASED PROBABILITY OF EXTINCTION DUE TO DECREASED GENETIC EFFECTIVE POPULATION SIZE: EXPERIMENTAL POPULATIONS OF CLARKIA PULCHELLA

We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (N_e), were maintained as isolated populations in a natural environment. After three generations, the low N_e treatment had significantly lower germination and survival rates than did the high N_e treatment. These lower germination and survival rates led to decreased mean fitness in the low N_e populations: estimated mean fitness in the low N_e populations was only 21% of the estimated mean fitness in the high N_e populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high N_e populations were still extant, whereas only 31% of the low N_e populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.     

THE EFFECTIVE SIZE OF A HIERARCHICALLY STRUCTURED POPULATION

A knowledge of the effective size of a population (N_e) is important in understanding its current and future evolutionary potential. Unfortunately, the effective size of a hierarchically structured population is not, in general, equal to the sum of its parts. In particular, the inbreeding structure has a major influence on N_e. Here I link N_e to Wright's hierarchical measures of inbreeding, F_IS and F_ST, for an island-structured population (or metapopulation) of size N_T. The influence of F_ST depends strongly on the degree to which island productivity is regulated. In the absence of local regulation (the interdemic model), interdemic genetic drift reduces N_e. When such drift is combined with local inbreeding under otherwise ideal conditions, the effects of F_IS and F_ST are identical: increasing inbreeding either within or between islands reduces N_e, with N_e = N_T/[(1 + F_IS)(1 + F_ST) ? 2F_ISF_ST]. However, if islands are all equally productive because of local density regulation (the traditional island model), then N_e = N_T/[(1 + F_IS)(1 –F_ST)] and the effect of F_ST is reversed. Under the interdemic model, random variation in the habitat quality (and hence productivity) of islands act to markedly decrease N_e. This variation has no effect under the island model because, by definition, all islands are equally productive. Even when no permanent island structure exists, spatial differences in habitat quality can significantly increase the overall variance in reproductive success of both males and females and hence lower N_e. Each of these basic results holds when other nonideal factors are added to the model. These factors, deviations from a 1:1 sex ratio, greater than Poisson variance in female reproductive success, and variation in male mating success due to polygynous mating systems, all act to lower N_e. The effects of male and female variance on N_e have important differences because only females affect island productivity. Finally, it is noted that to use these relationships, F_IS and F_ST must be estimated according to Wright's definition (and corrected to have a zero expectation under the null model). A commonly used partitioning (θ, θ_g) can be biased if either island size or the number of islands is small.     

EFFECTIVE POPULATION SIZE IN A CONTINUOUSLY DISTRIBUTED POPULATION

An individual-based simulation model was created to examine genetic variability, time until fixation and spatial genetic structure in a continuously distributed population. Previous mathematical models for continuously distributed populations have the difficulty that the assumption of independent reproduction and independent dispersal of offspring cause clumped spatial distribution and thus violate an assumption of random spatial distribution. In this study, this problem is avoided by considering the dispersal behavior of offspring. The simulation results showed that the inbreeding effective population size estimated by the rate of decrease of heterozygosity during the first 15 generations corresponds to the neighborhood size calculated by the standard deviation of the dispersal distance (σ_T). This inbreeding effective population size does not greatly change with the area of simulation when the densities and σ_T are the same. However, the inbreeding effective population size estimated by heterozygosity using the first 500 generations is larger than the neighborhood size calculated by the dispersal distance and increases with the area of simulation with the same densities. The variance effective population size, estimated by time until fixation of alleles, increases with dispersal distance (σ_T) and with the area of simulation given the same densities. The inbreeding effective population size and variance effective population size were smaller than the actual population size unless σ_T is sufficiently large (2 σ_T > approximate L/2, where L is a side of the simulation square).     

EFFECTIVE POPULATION SIZE AND THE FASTER-X EFFECT: AN EXTENDED MODEL

Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome ( N_eX ) is equal to three-quarters of the autosomal population size ( N_eA ). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X - linked and autosomal sites when this occurs. We find that N_eX/N_eA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when N_eX/N_eA > ³/₄. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution.     

THE INFLUENCE OF MATING SYSTEM AND OVERLAPPING GENERATIONS ON EFFECTIVE POPULATION SIZE

The effective population size (N_e) depends strongly on mating system and generation time. These two factors interact such that, under many circumstances, N_e is close to N/2, where N is the number of adults. This is shown to be the case for both simple and highly polygynous mating systems. The random union of gametes (RUG) and monogamy are two simple systems previously used in estimating N_e, and here a third, lottery polygyny, is added. Lottery polygyny, in which all males compete equally for females, results in a lower N_e than either RUG or monogamy! Given nonoverlapping generations the reduction is 33% for autosomal loci and 25% for sex-linked loci. The highly polygynous mating systems, harem polygyny and dominance polygyny, can give very low values of N_e/N when the generation time (T) is short. However, as T is lengthened, N_e approaches N/2. The influence of a biased sex ratio depends on the mating system and, in general, is not symmetrical. Biases can occur because of sex differences in either survival or recruitment of adults, and the potential for a sex-ratio bias to change N_e is much reduced given a survival bias. The number of juveniles present also has some influence: as the maturation time is lengthened, N_e increases.     

APPARENT SELECTIVE NEUTRALITY OF MITOCHONDRIAL DNA SIZE VARIATION: A TEST IN THE DEEP-SEA SCALLOP PLACOPECTEN MAGELLANICUS

Animal mitochondrial DNA (mtDNA) is believed to have evolved under intense selection for economy of the size of the molecule. Among scallop species mtDNA size may vary by a factor of two and among conspecific individuals by as much as 25%. We have examined the possibility that large mtDNA size differences may be associated with fitness in the deep sea scallop Placopecten magellanicus by comparing shell lengths of individuals with different copy numbers of a large mtDNA repeated sequence. Among juvenile cohorts of same age, shell length is known to be a good index of overall fitness in marine bivalves and it is shown here to be affected by differences in nuclear genotype, expressed as the degree of enzyme heterozygosity. We have observed no correlation between shell length and mtDNA length and interpreted this to mean that variation in the size of animal mtDNA is effectively neutral to the forces of natural selection acting on the individual. This type of mtDNA variation must, therefore, be explained in terms of biases in the molecular mechanisms causing expansion or contraction of the molecule, differential replication rates of mtDNA molecules of different size, and the stochastic assortment of mtDNA size classes among individuals.     

INBREEDING AND VARIANCE EFFECTIVE SIZES FOR NONRANDOM MATING POPULATIONS

Following an inbreeding approach and assuming discrete generations and autosomal inheritance involving genes that do not affect viability or reproductive ability, I have derived expressions for the inbreeding effective size, N_eI, for a finite diploid population with variable census sizes for three cases: monoecious populations with partial selfing; dioecious populations of equal numbers of males and females with partial sib mating; and unequal numbers of males and females with random mating. For the first two cases, recurrence equations for the inbreeding coefficient are also obtained, which allow inbreeding coefficients to be predicted exactly in both early and late generations. Following the variance of change in gene frequency approach, a general expression for variance effective size, N_eV, is obtained for a population with unequal numbers of male and female individuals, arbitrary family size distribution, and nonrandom mating. All the parameters involved are allowed to change over generations. For some special cases, the equation reduces to the simple expressions approximately as derived by previous authors. Comparisons are made between equations derived by the present study and those obtained by previous authors. Some of the published equations for N_eI and N_eV are shown to be incomplete or incorrect. Stochastic simulations are run to check the results where disagreements with others are involved.     

THE EFFECTS OF POPULATION BOTTLENECKS ON CLONAL INTERFERENCE, AND THE ADAPTATION EFFECTIVE POPULATION SIZE

Clonal interference refers to the competition that arises in asexual populations when multiple beneficial mutations segregate simultaneously. A large body of theoretical and experimental work now addresses this issue. Although much of the experimental work is performed in populations that grow exponentially between periodic population bottlenecks, the theoretical work to date has addressed only populations of a constant size. We derive an analytical approximation for the rate of adaptation in the presence of both clonal interference and bottlenecks, and compare this prediction to the results of an individual-based simulation, showing excellent agreement in the parameter regime in which clonal interference prevails. We also derive an appropriate definition for the effective population size for adaptive evolution experiments in the presence of population bottlenecks. This "adaptation effective population size" allows for a good approximation of the expected rate of adaptation, either in the strong-selection weak-mutation regime, or when clonal interference comes into play. In the multiple mutation regime, when the product of the population size and mutation rate is extremely large, these results no longer hold.     

OPPORTUNITY FOR SEXUAL SELECTION AND EFFECTIVE POPULATION SIZE IN THE LEK-BREEDING EUROPEAN TREEFROG (HYLA ARBOREA).

Sexual selection in lek-breeding species might drastically lower male effective population size, with potentially important consequences for evolutionary and conservation biology. Using field-monitoring and parental-assignment methods, we analyzed sex-specific variances in breeding success in a population of European treefrogs, to (1) help understanding the dynamics of genetic variance at sex-specific loci, and (2) better quantify the risk posed by genetic drift in this species locally endangered by habitat fragmentation. The variance in male mating success turned out to be markedly lower than values obtained from other amphibian species with polygamous mating systems. The ratio of effective breeding size to census breeding size was only slightly lower in males (0.44) than in females (0.57), in line with the patterns of genetic diversity previously reported from H. arborea sex chromosomes. Combining our results with data on age at maturity and adult survival, we show that the negative effect of the mating system is furthermore compensated by the effect of delayed maturity, so that the estimated instantaneous effective size broadly corresponded to census breeding size. We conclude that the lek-breeding system of treefrogs impacts only weakly the patterns of genetic diversity on sex-linked genes and the ability of natural populations to resist genetic drift.     

POPULATION STRUCTURE OF DIPODOMYS INGENS (HETEROMYIDAE): THE ROLE OF SPATIAL HETEROGENEITY IN MAINTAINING GENETIC DIVERSITY

The giant kangaroo rat, Dipodomys ingens (Heteromyidae), is an endangered rodent that inhabits approximately 3% of its estimated historic range. Its current distribution is centered in two geographic areas, situated about 150 km apart, in south-central California. We sequenced a 293 base-pair fragment at the 5' end of the control region in 95 giant kangaroo rats from nine localities to examine the genetic structure of extant populations. We determine that mutations in this section of the control region follow a negative binominal distribution, rather than a Poisson. However, the distance between haplotypes is small enough that the difference between a tree that corrects for the non-Poisson distribution of mutations and one that does not, is minimal. This implies that the use of methods that assume a Poisson distribution of mutations, such as those based on coalescent theory, are justified. We find that the correlation between levels of genetic diversity and estimated census size is poor. This suggests that population sizes have fluctuated over time or that populations have not been isolated from one another, or both. We also examine the hierarchical structure of populations and find that the southern populations are not genetically subdivided but that there is significant subdivision between northern and southern populations and between some northern subpopulations. The phylogeographic relationship between northern and southern populations can primarily be attributed to isolation by distance, although the time since divergence between them appears to be less than the age of either. To examine the phylogeographic relationships in more detail we construct a minimum spanning tree based on Tamura-Nei gamma-corrected distances and superimpose on it the geographic position of haplotypes. This reveals that there is more genetic distance between some northern haplotypes than between any northern and southern haplotypes, despite the geographic distance separating north from south and the larger size of the southern population. It also reveals that one northern population, in the Panoche Valley, contains old allelic lineages and shares ancestral polymorphism with several other populations. It also shows that two, small, geographically remote populations contain a surprising amount of genetic diversity, but that different population/geographic processes have affected the structure of that diversity. We estimate the average migration rate among all populations to be 7.5 per generation, and conclude that a disproportionate number of migration events involve gene flow with one northern population, the Panoche Valley. We find evidence for the hypothesis that there has been an increase in population size in the remaining populations in the north and suggest that the Panoche Valley could play a role in these expansions. Finally we discuss the probabilitiy that the genetic structure of the southern populations has been affected by fluctuations in size. These results are briefly compared to other studies on the genetic structure of rodent populations.     

SIZE STRUCTURE AND DYNAMICS IN A POPULATION OF SARGASSUM MUTICUM (PHAEOPHYCEAE)

Sargassum muticum (Yendo) Fensholt is an introduced brown seaweed with a very distinctive seasonal growth cycle on European shores. The present study links the dynamics of a population of S. muticum with the seasonal growth cycle of the species and the density-dependent processes operating throughout this cycle. Results indicate that both growth cycle and intraspecific competition influenced the structure and population dynamics. Size inequality increased during the slow growth phase (autumn–winter) of the 2-year study. Mechanisms generating inequality of size could be the existence of asymmetric competition and the inherent differences in growth rates between old (regenerated) and new thalli (recruits). Inequality of size distributions decreased progressively during the last months of the growth phase (spring–summer) and could be related to a process of self-thinning. There was a negative biomass–density relationship (as a measure of biomass accumulation-driven mortality) that confirms the importance of self-thinning as a major demographic factor in the S. muticum population.