Temporal change in the genetic structure between and within cohorts of a marine fish,Diplodus sargus,induced by a large variance in individual reproductive success

Temporal changes at 16 allozyme loci in the Diplodus sargus population of Banyuls-sur-Mer (Mediterranean Sea, France) were monitored. Temporal genetic variation within a single population was examined over two temporal scales: (i) among three year-classes sampled at the same age, and (ii) within a single year-class sampled three times over a two-year period. We observed a significant change in the genotypic structure within the same cohort during the first two years following settlement and before recruitment into the adult population. In addition, comparison of year-classes showed that cohorts differed significantly one year after settlement, whereas they became similar later on before recruitment into the adult population. The observed changes in the genetic structure within and between year-classes may be the result of complex selective processes or genetic drift. Linkage disequilibrium and genetic relatedness data suggest that these changes are due to large variation in reproductive success, followed by homogenization through adult movement. Overall, these results demonstrated a rapid genetic change within a population.     

Inbreeding in reintroduced populations: the effects of early reintroduction history and contemporary processes

Maintaining genetic variation and minimizing inbreeding are central goals of conservation genetics. It is therefore crucial to understand the important population parameters that affect inbreeding, particularly in reintroduction programs. Using data from 41 reintroduced Alpine ibex (Capra ibex ibex) populations we estimated inbreeding since the beginning of reintroductions using population-specific Fst, and inbreeding over the last few generations with contemporary effective population sizes. Total levels of inbreeding since reintroduction of ibex were, on average, close to that from one generation of half-sib mating. Contemporary effective population sizes did not reflect total inbreeding since reintroduction, but 16% of variation in contemporary effective population sizes among populations was due to variation in current population sizes. Substantial variation in inbreeding levels among populations was explained by founder group sizes and the harmonic mean population sizes since founding. This study emphasizes that, in addition to founder group sizes, early population growth rates are important parameters determining inbreeding levels in reintroduced populations.     

Relationship between abundance, growth, egg size and fecundity in a landlocked population of longfin smelt, Spirinchus thaleichthys

Sixteen year-classes of longfin smelt, Spirinchus thaleichthys , show a consistent pattern of alternating year-class strength between even (strong) and odd (weak) years. A recent (1989) odd year-class grew as well as, if not better than, the late 1960s odd year-classes. However, fish in the even year-classes (1988 and 1990) were significantly smaller in size then the 1966 and 1968 cohorts. Associated with this reduction in growth of the even year-class fish is a decline in fecundity. Fecundity of the odd year-classes of smelt was also smaller than in the early 1960s. Mean egg diameter and gonadosomatic index were not statistically different between 1988 and 1989 year-classes but the relative fecundity was higher for the 1988 year-class than for 1989, suggesting a higher reproductive investment in the even year-class. Reduction in growth and associated reproductive traits is considered to result from a reduction in the abundance of mysids, a preferred prey species.     

Craniometric variation,genetic theory,and modern human origins

Recent controversies surrounding models of modern human origins have focused on among-group variation, particularly the reconstruction of phylogenetic trees from mitochondrial DNA (mtDNA) and, the dating of population divergence. Problems in tree estimation have been seen as weakening the case for a replacement model and favoring a multiregional evolution model. There has been less discussion of patterns of within-group variation, although the mtDNA evidence has consistently shown the greatest diversity within African populations. Problems of interpretation abound given the numerous factors that can influence within-group variation, including the possibility of earlier divergence, differences in population size, patterns of population expansion, and variation in migration rates. We present a model of within-group phenotypic variation and apply it to a large set of craniometric data representing major Old World geographic regions (57 measurements for 1,159 cases in four regions: Europe, Sub-Saharan Africa, Australasia, and the Far East). The model predicts a linear relationship between variation within populations (the average within-group variance) and variation between populations (the genetic distance of populations to pooled phenotypic means). On a global level this relationship should hold if the long-term effective population sizes of each region are correctly specified. Other potential effects on withingroup variation are accounted for by the model. Comparison of observed and expected variances under the assumption of equal effective sizes for four regions indicates significantly greater within-group variation in Africa and significantly less within-group variation in Europe. These results suggest that the long-term effective population size was greatest in Africa. Closer examination of the model suggests that the long-term African effective size was roughly three times that of any other geographic region. Using these estimates of relative population size, we present a method for analyzing ancient population structure, which provides estimates of ancient migration. This method allows us to reconstruct migration history between geographic regions after adjustment for the effect of genetic drift on interpopulational distances. Our results show a clear isolation of Africa from other regions. We then present a method that allows direct estimation of the ancient migration matrix, thus providing us with information on the actual extent of interregional migration. These methods also provide estimates of time frames necessary to reach genetic equilibrium. The ultimate goal is extracting as much information from present-day patterns of human variation relevannt to issues of human origins. Our results are in agreement with mismatch distribution analysis of mtDNA, and they support a “weak Garden o Eden” model. In this model, modern-day variation can be explained by divergence from an initial source (perhaps Africa) into a number o small isolated populations, followed by later population expansion throughout our species. The major populationn expansions of Homo sapiens during and after the late Pleistocene have had the effect of “freezing” ancient patterns of population structure. While this is not the only possible scenario, we do note the close agreement with ecent analyses of mtDNA mismatch distibutions. © 1994 Wiley-Liss, Inc.     

Evolution of Size-Dependent Flowering in Onopordum illyricum: A Quantitative Assessment of the Role of Stochastic Selection Pressures

We explore the evolution of delayed, size-dependent reproduction in the monocarpic perennial Onopordum illyricum, using a range of mathematical models, parameterized with long-term field data. Analysis of the long-term data indicated that mortality, flowering, and growth were age and size dependent. Using mixed models, we estimated the variance about each of these relationships and also individual-specific effects. For the field populations, recruitment was the main density-dependent process, although there were weak effects of local density on growth and mortality. Using parameterized growth models, which assume plants grow along a deterministic trajectory, we predict plants should flower at sizes approximately 50% smaller than observed in the field. We then develop a simple criterion, termed the "1-yr look-ahead criterion," based on equating seed production now with that of next year, allowing for mortality and growth, to determine at what size a plant should flower. This model allows the incorporation of variance about the growth function and individual-specific effects. The model predicts flowering at sizes approximately double that observed, indicating that variance about the growth curve selects for larger sizes at flowering. The 1-yr look-ahead approach is approximate because it ignores growth opportunities more than 1 yr ahead. To assess the accuracy of this approach, we develop a more complicated dynamic state variable model. Both models give similar results indicating the utility of the 1-yr look-ahead criterion. To allow for temporal variation in the model parameters, we used an individual-based model with a genetic algorithm. This gave very accurate prediction of the observed flowering strategies. Sensitivity analysis of the model suggested that temporal variation in the parameters of the growth equation made waiting to flower more risky, so selected for smaller sizes at flowering. The models clearly indicate the need to incorporate stochastic variation in life-history analyses.     

The critical-period concept for juvenile survival and its relevance for population regulation in young sea trout, Salmo trutta

An example of density-dependent regulation is provided by a long-term investigation (1966-present) of a population of migratory trout (estuarine and sea trout), Salmo trutta L., in a Lake District stream. Evidence for the concept of a critical period for the survival of young fish is briefly reviewed and found to be rather equivocal. The concept is, however, relevant to the trout population. Loss rates were high before but low after a critical survival time ( t_c days after fry emergence) that varied between year-classes (range 33-70 days) and was inversely density-dependent on egg density. Survivor density and loss rates were strongly density-dependent on egg density before t _c, but proportionate survival with stable loss-rates occurred after t _c. Some trout established feeding territories soon after emergence and the number of fish without territories decreased from a high initial value to a negligible value at t _c. Fish size at t_c was not constant but increased as t _c increased. The range of t _c for the different year-classes was similar to that for survival times of unfed fry in the laboratory. A new stock-recruitment model, incorporating t _c, has been developed for the trout population and shown to be related to the model (Ricker curve) used in the long-term study. The critical time can also be regarded as the critical age for survival in young trout; this concept may be relevant to other fish species.     

A note on the growth-rate and year-class strength of bream, Abramis brama (L.), in three eutrophic lakes, England

In this study some comparative observations on the growth-rate and year-class strength of bream, Abramis brama , in three Shropshire-Cheshire meres are given. All populations are exposed to variable recruitment. The occurrence of four strong year-classes (1959, 1966, 1969,1973) suggests that climate is an important factor influencing spawning success. Water temperatures ≥16°C in July and August may be particularly important. All other intervening year-classes are absent. The growth-rate of bream in Tatton Mere and Ellesmere Mere is good ( L ∞= 541–561 mm) but comparatively poor ( L ∞= 448 mm) in Cole Mere. The significance of population density, food supply and parasitic infestation by Ligula intestinalis is discussed.     

Effective Population Sizes with Multiple Paternity

While the concept of effective population size is of obvious applicability to many questions in population genetics and conservation biology, its utility has suffered due to a lack of agreement among its various formulations. Often, mathematical formulations for effective sizes apply restrictive assumptions that limit their applicability. Herein, expressions for effective sizes of populations that account for mating tactics, biases in sex ratios, and differential dispersal rates (among other parameters) are developed. Of primary interest is the influence of multiple paternity on the maintenance of genetic variation in a population. In addition to the standard inbreeding and variance effective sizes, intragroup (coancestral) and intergroup effective sizes also are developed. Expressions for effective sizes are developed for the beginning of nonrandom gene exchanges (initial effective sizes), the transition of gene correlations (instantaneous effective sizes), and the steady-state (asymptotic effective size). Results indicate that systems of mating that incorporate more than one male mate per female increase all effective sizes above those expected from polygyny and monogamy. Instantaneous and asymptotic sizes can be expressed relative to the fixation indices. The parameters presented herein can be utilized in models of effective sizes for the study of evolutionary biology and conservation genetics.     

Demographic Genetics of Brown Trout (Salmo Trutta) and Estimation of Effective Population Size from Temporal Change of Allele Frequencies

We studied temporal allele frequency shifts over 15 years and estimated the genetically effective size of four natural populations of brown trout (Salmo trutta L.) on the basis of the variation at 14 polymorphic allozyme loci. The allele frequency differences between consecutive cohorts were significant in all four populations. There were no indications of natural selection, and we conclude that random genetic drift is the most likely cause of temporal allele frequency shifts at the loci examined. Effective population sizes were estimated from observed allele frequency shifts among cohorts, taking into consideration the demographic characteristics of each population. The estimated effective sizes of the four populations range from 52 to 480 individuals, and we conclude that the effective size of natural brown trout populations may differ considerably among lakes that are similar in size and other apparent characteristics. In spite of their different effective sizes all four populations have similar levels of genetic variation (average heterozygosity) indicating that excessive loss of genetic variability has been retarded, most likely because of gene flow among neighboring populations.     

The effect of life-history and mode of inheritance on neutral genetic variability

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.     

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

Adaptation in eukaryotes is generally assumed to be mutation-limited because of small effective population sizes. This view is difficult to reconcile, however, with the observation that adaptation to anthropogenic changes, such as the introduction of pesticides, can occur very rapidly. Here we investigate adaptation at a key insecticide resistance locus (Ace) in Drosophila melanogaster and show that multiple simple and complex resistance alleles evolved quickly and repeatedly within individual populations. Our results imply that the current effective population size of modern D. melanogaster populations is likely to be substantially larger (≥100-fold) than commonly believed. This discrepancy arises because estimates of the effective population size are generally derived from levels of standing variation and thus reveal long-term population dynamics dominated by sharp—even if infrequent—bottlenecks. The short-term effective population sizes relevant for strong adaptation, on the other hand, might be much closer to census population sizes. Adaptation in Drosophila may therefore not be limited by waiting for mutations at single sites, and complex adaptive alleles can be generated quickly without fixation of intermediate states. Adaptive events should also commonly involve the simultaneous rise in frequency of independently generated adaptive mutations. These so-called soft sweeps have very distinct effects on the linked neutral polymorphisms compared to the standard hard sweeps in mutation-limited scenarios. Methods for the mapping of adaptive mutations or association mapping of evolutionarily relevant mutations may thus need to be reconsidered.     

Genetic evidence for larger African population size during recent human evolution

Genetic evidence suggests that the long-term average effective size of sub-Saharan Africa is larger than other geographic regions. A method is described that allows estimation of relative long-term regional population sizes. This method is applied to 60 microsatellite DNA loci from a sample of 72 sub-Saharan Africans, 63 East Asians, and 120 Europeans. Average heterozygosity is significantly higher in the sub-Saharan African sample. Expected heterozygosity was computed for each region and locus using a population genetic model based on the null hypothesis of equal long-term population sizes. Average residual heterozygosity is significantly higher in the sub-Saharan African sample, indicating that African population size was larger than other regions during recent human evolution. The best fit of the model is with relative population weights of 0.73 for sub-Saharan Africa, 0.09 for East Asia, and 0.18 for Europe. These results are similar to those obtained using craniometric variation for these three geographic regions. These results, combined with inferences from other genetic studies, support a major role of Africa in the origin of modern humans. It is less clear, however, whether complete African replacement is the most appropriate model. An alternative is an African origin with non-African gene flow. While Africa is an important region in recent human evolution, it is not clear whether the gene pool of our species is completely out of Africa or predominately out of Africa.     

Some characteristics of a pike Esox lucius L. population in an Irish reservoir

A study of a stocked upland reservoir trout fishery, using gill nets, revealed the presence of a large stock of pike and poor trout numbers. The overall growth rate of pike was slow. Two year-classes of pike dominated, but the broad age and length frequency ranges, and the high average weight of individuals were indicative of an unexploited stock. Higher than normal water levels during the spawning period and into the summer period in both 1985 and 1986, coincided with the dominant pike year-classes recorded several years later. This revised version was published online in July 2006 with corrections to the Cover Date.     

The role of temperature and cannibalism in interannual recruitment variation of bass in British waters

Between-year variation in bass Dicentrarchus labrax year-class strength in southern British waters is investigated. Mean spring-summer seawater temperature in the year of birth was significantly positively correlated with both the level of summer recruitment of the 0 + group to the estuarine nurseries and subsequent recruitment of III + fish to the adult population. Spectral analysis of the temperature-compensated time series showed that a statistically significant proportion of the variation not attributable to temperature was periodic at 0–33 cycles year⁻¹. Therefore, a simple, three-parameter model, combining a linear relationship between temperature and abundance and a second-order autoregressive model can be used to describe and predict variation in relative adult YCS. Bass remain for their first 3 years within their estuarine nursery areas. As I + fish were observed in Southampton water to cannibalize the 0 + group, it is suggested that strong year-classes suppress recruitment for the next 2 years even if the temperature is suitable to promote a strong year-class. Cyclic variation in recruitment caused by intraspecific interactions, particularly cannibalism, may be a feature of other marine fish that use estuaries as nursery areas.     

A 9-year study of the life cycle of Ephemera danica Müll. (Ephemeridae: Ephemeroptera) in the River Lambourn, England

Abstract. 1. The life cycle of the mayfly, Ephemera danica , was studied on two contrasted sites on the River Lambourn between 1971 and 1979.
2. Quantitative samples of nymphs were taken on the five major biotopes of the river bed, gravel, silt, Ranunculus, Berula and Callitriche . Exposed areas of gravel and silt held significantly lower densities of nymphs than the three macro-phytes with their underlying substrata. The sandy substratum underlying beds of Berula frequently held significantly higher densities than the other macrophytes.
3. Monthly samples from March 1971 to April 1972 followed by samples in June and December from 1972 to 1979 indicated that the nymphal phase normally took 2 years in the River Lambourn.
4. All odd-numbered years from 1971 to 1979 produced weak year-classes. In contrast, all even-numbered years between 1970 and 1978, with the exception of 1972, produced relatively strong year-classes.
5. Meteorological data for the period of flight activity in E.danica indicated that conditions were colder and damper in 1972 than in the other even-numbered years of the study, when recruitment was more successful.     

Beyond the beneficial effects of translocations as an effective tool for the genetic restoration of isolated populations

Translocations are becoming increasingly popular as appropriate management strategies for the genetic restoration of endangered species and populations. Although a few studies have shown that the introduction of novel alleles has reversed the detrimental effects of inbreeding over the short-term (i.e., genetic rescue), it is not clear how effective such translocations are for both maintaining neutral variation that may be adaptive in the future (i.e., genetic restoration) and increasing population viability over the long-term. In addition, scientists have expressed concerns regarding the potential genetic swamping of locally adapted populations, which may eliminate significant components of genetic diversity through the replacement of the target population by the source individuals used for translocations. Here we show that bird translocations into a wild population of greater prairie-chickens (Tympanuchus cupido pinnatus) in southeastern Illinois were effective in both removing detrimental variation associated with inbreeding depression as well as restoring neutral genetic variation to historical levels. Furthermore, we found that although translocations resulted in immediate increases in fitness, the demographic recovery and long-term viability of the population appears to be limited by the availability of suitable habitat. Our results demonstrate that although translocations can be effective management tools for the genetic restoration of wild populations on the verge of extinction, their long-term viability may not be guaranteed unless the initial conditions that led to most species declines (e.g., habitat loss) are reversed.     

Long-term studies on the Windermere populations of perch (Perca fluviatilis), pike (Esox lucius) and Arctic charr (Salvelinus alpinus)

SUMMARY. 1, Windermere is a glacial valley lake with two basins separated by shallows and a total area of 14.8 km². Perch, pike and charr are the dominant fish species and have been studied on a continuous basis for over 45 years.
2. The initial slow-growing stocks of numerous small perch and moderate numbers of large pike were subjected to a heavy initial fishing pressure that was subsequently relaxed for perch but not for larger (>550 mm) pike. The number of charr in the lake has increased 6–8-fold during the study, probably due to the sustained reduction in the abundance of the larger pike that heavily predate the autumn spawning race of charr when it enters the shallow littoral areas to spawn.
3. The biomass of perch did not recover from the initial fishery until the late 1950s when strong year-classes occurred in warm summers. However, it was now composed of larger and faster growing individuals. In 1976, disease killed over 98% of all adult perch in the lake and the subsequent recovery has again been slow.
4. Existing models have explained the variation in perch year-class strength for the years 1959–74 in terms of adult perch biomass, pike cohort strength and temperature in the year of hatch. A new. more generally applicable model, incorporating a stock-recruitment expression, gives a better fit to the earlier data, particularly from the North Basin, where there have been periods of extremely low adult biomass.
5. The importance of continuing to extend these long-term data sets and the scope for future modelling work are discussed.     

On the estimation of ancestral population sizes of modern humans

The theory developed by Takahata and colleagues for estimating the effective population size of ancestral species using homologous sequences from closely related extant species was extended to take account of variation of evolutionary rates among loci. Nuclear sequence data related to the evolution of modern humans were reanalysed and computer simulations were performed to examine the effect of rate variation on estimation of ancestral population sizes. It is found that the among-locus rate variation does not have a significant effect on estimation of the current population size when sequences from multiple loci are sampled from the same species, but does have a significant effect on estimation of the ancestral population size using sequences from different species. The effects of ancestral population size, species divergence time and among-locus rate variation are found to be highly correlated, and to achieve reliable estimates of the ancestral population size, effects of the other two factors should be estimated independently.     

The relative influences of host plant genotype and yearly abiotic variability in determining herbivore abundance

Both plant genotype and yearly abiotic variation affect herbivore population sizes, but long-term data have rarely been used to contrast the relative contributions of each. Using a hierarchical Bayesian model, we directly compare effects of these two factors on the population size of a common herbivore, Aceria parapopuli, on Populus angustifolia × fremontii F₁ hybrid trees growing in a common garden across 8 years. Several patterns emerged. First, the Bayesian posterior estimates of tree genotype effects on mite gall number ranged from 0.0043 to 229 on a linear scale. Second, year effect sizes across 8 years of study ranged from 0.133 to 1.895. Third, in comparing the magnitudes of genotypic versus yearly variation, we found that genotypic variation was over 130 times greater than variation among years. Fourth, precipitation in the previous year negatively affected gall abundances, but was minimal compared to tree genotype effects. These findings demonstrate the relative importance of tree genotypic variation in determining herbivore population size. However, given the demonstrated sensitivity of cottonwoods to drought, the loss of individual tree genotypes from an altered climate would have catastrophic impacts on mites that are dependent upon these genotypes for their survival.     

Extrinsic factors and the population sizes of threatened birds

Attempts to explain the orders-of-magnitude variation observed in animal population sizes have principally focused on intrinsic differences between the taxa compared, but with limited success: most variation remains unexplained by such studies. However, animal population sizes may also vary in response to extrinsic factors, such as the environment occupied or the influence of human activities. Here, we use new estimates of the global population sizes of threatened bird species to examine extrinsic correlates of variation in their numbers, using general linear modelling and methods to control for phylogenetic relatedness. Threatened bird population sizes varied significantly with several extrinsic factors, including altitude, biogeographical region inhabited, type of extinction threat faced, and habitat used. They also vary with geographical range size, which was included in the analysis to control for its potentially confounding effects on the results. Details of the observed relationships, which vary with analytical method, are discussed. However, apart from geographical range size, none of the extrinsic variables analysed here explain more than a small percentage of the variation in threatened bird population sizes. Thus, it seems likely that a comprehensive explanation for why some species are common while others are rare will not be dominated by a single factor.