THE DISTINCTIVE FOOTPRINTS OF LOCAL HITCHHIKING IN A VARIED ENVIRONMENT AND GLOBAL HITCHHIKING IN A SUBDIVIDED POPULATION

Loci with higher levels of population differentiation than the neutral expectation are traditionally interpreted as evidence of ongoing selection that varies in space. This article emphasizes an alternative explanation that has been largely overlooked to date: in species subdivided into large subpopulations, enhanced differentiation can also be the signature left by the fixation of an unconditionally favorable mutation on its chromosomal neighborhood. This is because the hitchhiking effect is expected to diminish as the favorable mutation spreads from the deme in which it originated to other demes. To discriminate among the two alternative scenarios one needs to investigate how genetic structure varies along the chromosomal region of the locus. Local hitchhiking is shown to generate a single sharp peak of differentiation centered on the adaptive polymorphism and the standard signature of a selective sweep only in those subpopulations in which the allele is favored. Global hitchhiking produces two domes of differentiation on either side of the fixed advantageous mutation and signatures of a selective sweep in every subpopulation, albeit of different magnitude. Investigating population differentiation around a locus that strongly differentiates two otherwise genetically similar populations of the marine mussel Mytilus edulis, plausible evidence for the global hitchhiking hypothesis has been obtained. Global hitchhiking is a neglected phenomenon that might prove to be important in species with large population sizes such as many marine invertebrates.     

MAXIMUM-LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION

In this paper we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's F_ST statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the F_ST-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypotheses such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data.     

POPULATION GENETICS OF A PARASITIC CHROMOSOME: EXPERIMENTAL ANALYSIS OF PSR IN SUBDIVIDED POPULATIONS

Nasonia vitripennis is a parasitoid wasp that harbors several non-Mendelian sex-ratio distorters. These include MSR (Maternal Sex Ratio), a cytoplasmic element that causes nearly all-female families, and PSR (Paternal Sex Ratio), a supernumerary chromosome that causes all-male families. As in other hymenoptera, N. vitripennis has haplodiploid sex determination. Normally, unfertilized (haploid) eggs develop into males and fertilized (diploid) eggs develop into females. The PSR chromosome violates this normal pattern; it is inherited through sperm, but then causes destruction of the paternal chromosomes (except itself), thus converting diploid fertilized eggs (normally females) into haploid eggs that develop into PSR-bearing males. PSR is an extreme example of “parasitic” or “selfish” DNA. Because N. vitripennis has a highly subdivided population structure in nature, population-level selection may be important in determining the dynamics of PSR in natural populations. A theoretical analysis shows that subdivided population structure reduces PSR frequency, whereas high fertilization proportion (such as produced by the MSR element) increases PSR frequency. Population experiments using two deme sizes (3- and 12-foundress groups) and strains producing two fertilization proportions [wild-type (LabII)–57–67% female, and MSR (MI)–90–93% female] confirm these predictions. PSR achieved frequencies over 0.90 in 12–foundress group MSR populations in contrast to 0.20–0.40 in wild-type 12–foundress populations. PSR was selected against in wild-type populations composed of three-foundress groups. In MSR populations with three-foundress groups, presence of PSR selected against the MSR cytoplasmic element, eventually leading to low frequencies of both PSR and MSR. Complicated dynamics may occur when these two sex-ratio distorters are both present in highly subdivided populations. The existence of PSR in natural populations may depend on the presence of MSR. Results indicate that population subdivision could be important in determining the frequency of sex ratio distorters in N. vitripennis.     

THE PROBABILITY OF FIXATION OF A NEW KARYOTYPE IN A CONTINUOUS POPULATION

We investigate the probability of fixation of a chromosome rearrangement in a subdivided population, concentrating on the limit where migration is so large relative to selection (m ? s) that the population can be thought of as being continuously distributed. We study two demes, and one- and two-dimensional populations. For two demes, the probability of fixation in the limit of high migration approximates that of a population with twice the size of a single deme: migration therefore greatly reduces the fixation probability. However, this behavior does not extend to a large array of demes. Then, the fixation probability depends primarily on neighborhood size (Nb), and may be appreciable even with strong selection and free gene flow (≈exp(-B ≈ Nb√s) in one dimension, ≈exp(-B ≈ Nb) in two dimensions). Our results are close to those for the more tractable case of a polygenic character under disruptive selection.     

MACRO- AND MICROGEOGRAPHIC STRUCTURE OF A SPATIALLY SUBDIVIDED BEETLE SPECIES IN NATURE

Spatial subdivision of species can affect their population structure by allowing processes such as limited dispersal, spatial heterogeneity in selective pressures, small population sizes, and random events to operate. By studying species restricted to islands or “island” habitats, one can attempt to determine which of these factors have affected the current structure of the population. Collops georgianus (Coleoptera: Melyridae), a beetle species endemic to the “island” habitat of granitic rock outcrops, was chosen to see how its spatially subdivided distribution has affected its genetic structure. Its genetic structure was examined on both a macrogeographic and a microgeographic level using protein electrophoresis. Macrogeographically, 12 populations throughout its range were sampled. The discontinuous distribution of outcrops, and thus populations, throughout its range, has determined the connectivity of the populations. Significant variation in allele frequencies and substructuring (F_ST = 0.192) was found throughout the range, but there was no spatial autocorrelation. Microgeographically, in the central part of the range, where outcrops are denser and more continuously distributed in space, there was evidence of isolation by distance. Very little variation in allele frequencies was found, but a low but significant level of substructuring occurred among the populations. Comparison of disjunct and continuous populations microgeographically revealed no effect of disjunct distributions, although a significant effect of distance was detected. Effective population size variation among populations and between years, compounded with the effects of local extinctions, suggest that random processes such as drift and founder effects are important determinants of the population's genetic structure.     

FIXATION PROBABILITIES OF SELFING RATE MODIFIERS IN SIMULATIONS WITH SEVERAL DELETERIOUS ALLELES WITH LINKAGE

The fixation rates of selfing rate modifiers were found by stochastic simulation in an infinite site model, including effects of several deleterious alleles with variable effects, which were randomly distributed in the genome without assuming any pollen discounting. Previous results on the evolution of selfing obtained by more precise methods were in this study further validated, and it was concluded that the effect of genetic associations on the evolution of mating systems is small except in the case of full pollen discounting. Furthermore, attention was given to the uneven distribution of the genetic load in the population, and the accompanying large among-genome variation in fixation rates. This among-genome variation will be of significance for the evolution of mating systems.     

INBREEDING AS A STRATEGY IN SUBDIVIDED POPULATIONS

A generalized expression for coefficients of consanguinity and relationship with previous inbreeding is presented to examine various breeding strategies in subdivided populations. Conditions that would favor inbreeding are developed for: 1) nonfamilial inbreeding within a deme versus outbreeding; 2) altruistic inbreeding by females versus outbreeding; 3) sib-mating versus outbreeding; and 4) sib-mating versus nonfamilial breeding within a deme. Inbreeding behavior is advantageous under certain conditions but depends on the types of mating, the previous breeding history of the deme, the rate of accumulation of inbreeding depression, and the cost of migration. In polygynous mating systems it is genetically more advantageous for males to migrate, because female emigration may 1) leave a related male with no mate or one fewer mate, or 2) force both male and female to risk the cost of migration. Nonfamilial breeding is always a better strategy than sib-mating given previous inbreeding within the deme. Even when the cost of migration is zero, inbreeding is favored if the coefficient of relationship among relatives is greater than the ratio of the probabilities of offspring inviability to offspring viability. Although high inbreeding coefficients are probably not adaptive unless the costs of migration are great or inbreeding depression constants are small, low levels of inbreeding are advantageous in many situations. Therefore, increased genetic representation by way of inbreeding and inclusive fitness is a major component of the evolutionary process.     

EVOLUTION OF ALTRUISM IN KIN-STRUCTURED AND RANDOM SUBDIVIDED POPULATIONS

A. population structure favorable to the evolution of an altruistic trait is studied by Monte Carlo simulation. The model is based on a small-scale nonindustrial human society but seems generalizable to other highly social mammals. Three hierarchical levels are recognized: 1) the ecologically isolated local group (hamlet) which may be composed of kin and/or unrelated individuals; 2) the deme (settlement) comprising several such groups which interbreed; and 3) the set of demes (metapopulation) among which gene flow occurs. The first two levels of the model are based on D. S. Wilson's structured deme concept; the third allows for gene flow among demes in the metapopulation and for the structured diffusion of alleles across a wider area than might be included within the scope of a single deme. The simulation models genetic drift by a process of hamlet formation which may be random, or variously kin-structured. Hamlets may then become extinct based on a probability function of their gene frequencies. Individual selection within settlements is modeled deterministically, and gene flow among settlements is modeled as two-dimensional steppingstone migration of random or kin-structured groups. Results of the simulations show that, with realistic values for group sizes, moderate extinction rate, and high rates of migration (m > 27%), disadvantageous alleles (s = 10% and 25%) may increase markedly due to differential hamlet extinction over the course of 50 generations. The greater the degree of kin-structuring of founder groups, the higher the variance among hamlets and the faster the rate of increase of the allele for altruism. Nonetheless, even in some randomly founded groups, a clear increase in the altruism gene frequency occurred. It is also notable that kin-structured group selection by hamlet extinction may be effective when the initial frequency of altruism genes is very low (average of one per deme) and among a relatively small number of demes (25). Thus the process of group extinction in a hierarchically structured population allows rapid increase of an allele for altruism under plausible demographic conditions.     

PATTERNS OF GENETIC ARCHITECTURE FOR LIFE-HISTORY TRAITS AND MOLECULAR MARKERS IN A SUBDIVIDED SPECIES

Abstract Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with Q _ST generally exceeding G _ST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of Q _ST and G _ST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria , regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex .     

THE EFFECT OF COLLECTIVE DISPERSAL ON THE GENETIC STRUCTURE OF A SUBDIVIDED POPULATION

Correlated dispersal paths between two or more individuals are widespread across many taxa. The population genetic implications of this collective dispersal have received relatively little attention. Here we develop two‐sample coalescent theory that incorporates collective dispersal in a finite island model to predict expected coalescence times, genetic diversities, and F‐statistics. We show that collective dispersal reduces mixing in the system, which decreases expected coalescence times and increases F_ST. The effects are strongest in systems with high migration rates. Collective dispersal breaks the invariance of within‐deme coalescence times to migration rate, whatever the deme size. It can also cause F_ST to increase with migration rate because the ratio of within‐ to between‐deme coalescence times can decrease as migration rate approaches unity. This effect is most biologically relevant when deme size is small. We find qualitatively similar results for diploid and gametic dispersal. We also demonstrate with simulations and analytical theory the strong similarity between the effects of collective dispersal and anisotropic dispersal. These findings have implications for our understanding of the balance between drift–migration–mutation in models of neutral evolution. This has applied consequences for the interpretation of genetic structure (e.g., chaotic genetic patchiness) and estimation of migration rates from genetic data.     

THE INFLUENCE OF SELF-FERTILIZATION AND POPULATION DYNAMICS ON THE GENETIC STRUCTURE OF SUBDIVIDED POPULATIONS: A CASE STUDY USING MICROSATELLITE MARKERS IN THE FRESHWATER SNAIL BULINUS TRUNCATUS

The distribution of neutral genetic variability within and among sets of populations results from the combined actions of genetic drift, migration, extinction and recolonization processes, mutation, and the mating system. We here analyzed these factors in 38 populations of the hermaphroditic snail Bulinus truncatus. The sampling area covered a large part of the species range. The variability was analyzed using four polymorphic microsatellite loci. A very large number of alleles (up to 55) was found at the level of the whole study. Observed heterozygote deficiencies within populations are consistent with very high selfing rates, generally above 0.80, in all populations. These should depress the variability within populations, because of low effective size, genetic hitchhiking, and background selection, whatever the model of mutation assumed. However, that some populations exhibit much more variability than others suggests that historical demographic processes (e.g., population size variation, bottlenecks, or founding events) may play a significant role. A hierarchical analysis of the distribution of the variability across populations indicates a strong pattern of isolation by distance, whatever the geographical scale considered. Our analysis also illustrates how the mutation rate may affect population differentiation, as different mutation rates result in different levels of homoplasy at microsatellite loci. The effects of both genetic drift and gene flow vary with the temporal and spatial scales considered in B. truncatus populations.     

NONSYMBIOTIC AND SYMBIOTIC NITROGEN FIXATION IN A WEAKLY MINEROTROPHIC PEATLAND

The acetylene reduction assay was used to measure nonsymbiotic and symbiotic nitrogen fixation in a weakly minerotrophic peatland throughout the ice-free season. Nonsymbiotic nitrogen fixation was found in surface materials and subsurface peat. In surface materials, nitrogenase activity measured in the field contributed about 0.6 kg N ha^-1 yr^-1, was closely associated with Sphagnum, but was not correlated with temperature between 12 and 27 C. No cyanobacteria were found in association with Sphagnum. In subsurface peat, nitrogenase activity measured in situ contributed no more than 0.4 kg N ha^-1 yr^-1 and was closely correlated with temperature between 7 and 21 C. There were uncertainites in these measurements due to presence of ethylene oxidizing activity and a long time lag. Symbiotic nitrogen fixation was found only in actinomycete-induced root nodules of Myrica gale L. Legumes were absent and the few lichens present lacked nitrogenase activity. Based on acetylene reduction assays, Myrica gale fixed about 35 kg N ha^-1 yr^-1. Nitrogenase activity in Myrica gale showed a strong seasonal pattern which varied little during three consecutive years even though water levels varied substantially. Nitrogen input to the peatland from nonsymbiotic nitrogen fixation was only 15% the amount contributed by bulk precipitation. Symbiotic fixation, in contrast, contributed approximately six times the amount in bulk precipitation.     

羊奶果结瘤固氮特性研究

羊奶果根瘤多年生,初发生时呈2—3分又状,后经多次分叉生长,形成珊瑚状的根瘤簇,外形球状或扁球状,直径可达数厘米。根瘤固氮活性较高,全年平均固氮活性8.86微摩乙烯/克鲜瘤/小时。固氮活性秋夏较高,冬春较低。根瘤离体后固氮能力持续时间较长,可达9小时。固氮作用最适温度为30℃,低温使固氮活性显著下降,短时间高温(37℃)能提高根瘤固氮活性,但持续高温会抑制固氮活性。 羊奶果根瘤具有氢酶,表现出较高吸氢活性(9.52微摩氢/克鲜瘤/小时),且持续时间较长。外源氢能明显提高根瘤固氮活性,提高幅度达60％左右。 羊奶果各器官硝酸还原酶活力为根>根瘤>叶片>枝条,叶片NR活力呈季节性变化,秋夏较高,冬春较低。根瘤NR活力变化较大,且与根瘤固氮活性变化的趋势基本一致。     

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.     

CARBONIC ANHYDRASE AND CARBON FIXATION IN COCCOLITHOPHORIDS1

Rates of carbon fixation in coccolithophorids in culture, unlike many other algae, are carbon limited at ambient levels of dissolved inorganic carbon (DIC). Apparently, plants often rely on activity of carbonic anhydrase (CA) to raise the level of CO₂ in cells and achieve carbon saturation. However, CA activities in the coccolithophorids, Coccolithus (= Emiliania) huxleyi Lohmann and Hymenomonas (=Cricosphaera) carterae Braarud, were either not detectable or very low compared to activities in other systems, including other algae, higher plants, and representative animals. Furthermore, additions of CA to medium with 2 mM DIC at pH 8.1 resulted in nearly 30% enhancement of photosynthesis, but not coccolith formation. Although carbon fixation in coccolithophorids can be suppressed by the CA inhibitor acetazolamide, studies of CaCO₃ nucleation revealed a non-specific effect of the inhibitor. Using a 30 min assay based on pH decreases accompanying loss of dissolved. CO₃^2-, inhibition of crystal formation in the absence of CA at 1 mM acetazolamide was demonstrated for decalcified crab carapace, a tissue with which normal CaCo₃ deposition in vitro has been shown. The results suggest only a minor role for CA in coccolithophorids.     

FLUCTUATING SELECTION AND RESPONSE IN A POPULATION OF FRESHWATER COPEPODS

The timing of springtime production of diapausing eggs by a population of the freshwater copepod, Diaptomus sanguineus, has been shown previously to be consistent with avoidance of seasonally intense fish predation. Natural selection acting on the timing of diapause fluctuates between years depending upon the population density of fish. Here we show that, in the field, the mean timing of diapause shifts between years in response to fluctuations in selection. Diapause is earlier in years following high predator density, and is later in years following low predator density. Although selection intensity in individual years may be large, the mean intensity over the decade of fluctuating selection investigated here is close to zero. Photoperiod sensitivity of the diapausetiming trait is heritable in the laboratory. The combination of fluctuating selection and multi-generation storage of genotypes as diapausing eggs in lake sediments may contribute to the maintenance of the genetic variation that permits the rapid selection response seen in the field.