Impact of natural enemies on obligately cooperative breeders

Obligately cooperative breeders (cooperators) display a negative growth rate once they fall below a minimum density. Constraints imposed by natural enemies, such as predators or competitors, may push cooperator groups closer to this threshold, thus increasing the risk that stochastic fluctuations will drive them below it. This may indirectly drive these groups to extinction, thereby increasing the risk of population extinction. In this paper, we construct mathematical models of the dynamics of groups of cooperators and non-cooperators in the presence of two types of enemies: enemies whose dynamics do not depend on the dynamics of their victim (e.g., amensal competitor, generalist predator) and those whose dynamics do. In the latter case, we distinguish positive (e.g., specialist predator) and negative (e.g., bilateral competitor) reciprocal effects. These models correspond to the classical amensal, predation and competition models, in the presence of an Allee effect. We then develop the models to study consequences at the population level. By comparing models with or without an Allee effect, we show that enemies decrease the group size of cooperators more than that of non-cooperators, and this increases their group extinction risk. We also demonstrate how an Allee effect at a lower dynamical level can have consequences at a higher level: inverse density dependence at the group level generated lower population sizes and higher risks of population extinction. Our results also suggest that demographic compensation can be achieved by cooperators through an increased intrinsic growth rate, or by decreasing the enemy constraint. Both of these types of compensation have been observed in empirical studies of cooperators.     

Individual‐level leaf trait variation and correlation across biological and spatial scales

Even with increasing interest in the ecological importance of intraspecific trait variation (ITV) for better understanding ecological processes, few studies have quantified ITV in seedlings and assessed constraints imposed by trade‐offs and correlations among individual‐level leaf traits. Estimating the amount and role of ITV in seedlings is important to understand tree recruitment and long‐term forest dynamics. We measured ten different size, economics, and whole leaf traits (lamina and petiole) for more than 2,800 seedlings (height ≥ 10 cm and diameter at breast height < 1 cm) in 283 seedling plots and then quantified the amount of ITV and trait correlations across two biological (intraspecific and interspecific) and spatial (within and among plots) scales. Finally, we explored the effects of trait variance and sample size on the strength of trait correlations. We found about 40% (6%–63%) variation in leaf‐level traits was explained by ITV across all traits. Lamina and petiole traits were correlated across biological and spatial scales, whereas leaf size traits (e.g., lamina area) were weakly correlated with economics traits (e.g., specific lamina area); lamina mass ratio was strongly related to the petiole length. Trait correlations varied among species, plots, and different scales but there was no evidence that the strength of trait relationships was stronger at broader than finer biological and spatial scales. While larger trait variance increased the strength of correlations, the sample size was the most important factor that was negatively related to the strength of trait correlations. Our results showed that a large amount of trait variation was explained by ITV, which highlighted the importance of considering ITV when using trait‐based approaches in seedling ecology. In addition, sample size was an important factor that influenced the strength of trait correlations, which suggests that comparing trait correlations across studies should consider the differences in sample size.     

树木根系衰老研究的意义与现状

树木根系是树木重要的组成部分,具有养分和水分的吸收、传输和储存、树体的固定与支撑等重要的生理功能．在树木根系形成以后,常常遭遇到养分和水分胁迫,因此,其养分和水分的吸收功能尤其重要,在森林土壤中,养分和水分具有很大的时间和空间异质性,随着养分和水分在时间和空间上的变化,树木及时地主动调整其碳在根系中的分配,从而导致部分根系衰老或死亡,在林学上,树木根系衰老与养分和水分吸收关系密切,因而与树木生产力有直接的关系．在生态系统乃至全球尺度上,树木根系衰老影响碳循环和养分循环,因为根系对碳的消耗占树木通过光合作用所固定的碳的比例相当大,且含有丰富的养分．树木根系衰老受许多环境因子的影响,生物因子有真菌、细菌、病毒、土壤小型动物等,非生物因子有水分、温度、土壤养分、重金属等,这些因子对树木根系衰老的影响机制并不相同,尽管在树木根系衰老研究领域取得了长足的进步,提出了许多不同的假设,但仍有许多问题尚未解决,这些假设也需要更多的实验来验证,运用细胞学、生物化学、土壤科学、遗传学等多学科的交叉研究可进一步揭示根系衰老的本质。     

Transmission shifts underlie variability in population responses to Yersinia pestis infection

Host populations for the plague bacterium, Yersinia pestis, are highly variable in their response to plague ranging from near deterministic extinction (i.e., epizootic dynamics) to a low probability of extinction despite persistent infection (i.e., enzootic dynamics). Much of the work to understand this variability has focused on specific host characteristics, such as population size and resistance, and their role in determining plague dynamics. Here, however, we advance the idea that the relative importance of alternative transmission routes may vary causing shifts from epizootic to enzootic dynamics. We present a model that incorporates host and flea ecology with multiple transmission hypotheses to study how transmission shifts determine population responses to plague. Our results suggest enzootic persistence relies on infection of an off-host flea reservoir and epizootics rely on transiently maintained flea infection loads through repeated infectious feeds by fleas. In either case, early-phase transmission by fleas (i.e., transmission immediately following an infected blood meal) has been observed in laboratory studies, and we show that it is capable of driving plague dynamics at the population level. Sensitivity analysis of model parameters revealed that host characteristics (e.g., population size and resistance) vary in importance depending on transmission dynamics, suggesting that host ecology may scale differently through different transmission routes enabling prediction of population responses in a more robust way than using either host characteristics or transmission shifts alone.     

四川省缙云山栲树种群结构和动态的初步研究

 栲树(Castanopsis fargesii)是亚热带常绿阔叶林的建群种和优势种之一。本文应用相邻格子样方法和每木调查法进行野外抽样,对缙云山栲树种群的立木级结构和分布格局及其动态特点进行了分析,并探讨了研究长生命期常绿阔叶树种种群的方法问题。结果表明,应用立木级结构代替年龄结构研究栲树种群的结构和动态特征是适用的。立木级结构和存活曲线分析表明栲树种群具有增长型的动态特征。同时应用一次性的调查资料研究了栲树种群的分布格局及其动态特征,显示出栲树种群在其发育过程中,分布格局由集群分布向随机分布变化,而且这种变化是和种群的数量的动态变化有关。引起分布格局发生变化的主要原因是种内及种间竞争所导致的自疏和它疏。     

Guidelines for the design and statistical analysis of experiments using laboratory animals

For ethical and economic reasons, it is important to design animal experiments well, to analyze the data correctly, and to use the minimum number of animals necessary to achieve the scientific objectives---but not so few as to miss biologically important effects or require unnecessary repetition of experiments. Investigators are urged to consult a statistician at the design stage and are reminded that no experiment should ever be started without a clear idea of how the resulting data are to be analyzed. These guidelines are provided to help biomedical research workers perform their experiments efficiently and analyze their results so that they can extract all useful information from the resulting data. Among the topics discussed are the varying purposes of experiments (e.g., exploratory vs. confirmatory); the experimental unit; the necessity of recording full experimental details (e.g., species, sex, age, microbiological status, strain and source of animals, and husbandry conditions); assigning experimental units to treatments using randomization; other aspects of the experiment (e.g., timing of measurements); using formal experimental designs (e.g., completely randomized and randomized block); estimating the size of the experiment using power and sample size calculations; screening raw data for obvious errors; using the t-test or analysis of variance for parametric analysis; and effective design of graphical data.     

Inferring population history from genealogical trees

Inference about population history from DNA sequence data has become increasingly popular. For human populations, questions about whether a population has been expanding and when expansion began are often the focus of attention. For viral populations, questions about the epidemiological history of a virus, e.g., HIV-1 and Hepatitis C, are often of interest. In this paper I address the following question: Can population history be accurately inferred from single locus DNA data? An idealised world is considered in which the tree relating a sample of n non-recombining and selectively neutral DNA sequences is observed, rather than just the sequences themselves. This approach provides an upper limit to the information that possibly can be extracted from a sample. It is shown, based on Kingman's (1982a) coalescent process, that consistent estimation of parameters describing population history (e.g., a growth rate) cannot be achieved for increasing sample size, n. This is worse than often found for estimators of genetic parameters, e.g., the mutation rate typically converges at rate \(\) under the assumption that all historical mutations can be observed in the sample. In addition, various results for the distribution of maximum likelihood estimators are presented.     

Safe sites for tree regeneration in wooded pastures: A case of associational resistance?

Abstract. Question: Are tree saplings in wooded pastures spatially associated with specific nurse structures or plants that facilitate tree sapling survival? Location: Wooded pastures in the Jura Mountains, Switzerland. Methods: In two sites, 73 km apart, we sampled 294 plots of 4 m², systematically distributed on 1 ha. We recorded number and height of all established Picea abies saplings (> 1 a of age and up to 40 cm in height), and visually estimated cover of rocks, shrubs, tree stumps, overhanging tree branches and unpalatable plant species. Results: Despite differences in site characteristics, we found overall positive effects of cover of unpalatable plants, rocky outcrops and tree stumps on the density of Picea saplings. Plots with tree stumps and higher cover of rocky outcrops and unpalatable plants were more likely to contain Picea saplings. Conclusions: Unpalatable plants, rocky outcrops and tree stumps seem to form safe sites for Picea saplings in this grazed system, improving their establishment and survival. Our findings support the idea that associational resistance drives the dynamics of wooded pastures, but experimental evidence for this hypothesis is still required.     

Dietary niche and population dynamic feedbacks in a novel habitat

Population dynamics and resource use are often intricately connected via density‐dependent intraspecific competition. However, experimental studies of concurrent change in population and resource use dynamics are scarce. In particular, the impact of factors such as genetic diversity, which can affect both population dynamics and competition, remains unexplored. Using stable isotope analysis and periodic population censuses, we quantified both diet and population dynamics in wheat‐adapted Tribolium castaneum (flour beetle) populations provided with an additional novel resource (corn). Populations were initiated with different levels of genetic variation for traits relevant to population growth and resource use (e.g. fecundity and survival).We found that high population size decreased subsequent corn use, and high corn use in turn lowered population size. Surprisingly, we did not detect a significant effect of founding genetic variation on resource niche expansion, although genetic variation increased overall population size and stability. In contrast, dietary niche expansion decreased both population size and stability. Finally, larval and adult niche dynamics were uncorrelated, suggesting that various life stages perceive or respond differentially to intraspecific competition and resource availability. Our experiments indicate that population performance in a novel habitat depends on stage‐specific interactions between resource use, standing genetic variation, and population size.     

An instantaneous coalescent method insensitive to population structure

Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.     

Offspring size–number tradeoffs and food quality feedbacks impact population dynamics in a Daphnia–algae system

Population fluctuations can be affected by both extrinsic (e.g. weather patterns, food availability) and intrinsic (e.g. life‐history) factors. A key life‐history tradeoff is the production of offspring size versus number, ranging from many small offspring to few large offspring. Models show that this life‐history tradeoff in offspring size and number, through maturation time, can have significant impacts on population dynamics. However, few manipulative experiments have been conducted that can isolate life‐history effects from impacts of extrinsic factors in consumer–resource systems. We experimentally tested the effect of an offspring size–number tradeoff on population stability and food availability in a consumer–resource system. Using Daphnia pulex, we created a shift from many, small offspring being produced to fewer, larger offspring. Two sets of experiments were performed to examine the interaction of an extrinsic factor (light levels) and intrinsic population structure on dynamics, and we controlled for the ingestion pressure on algal prey at the time of the manipulation. We predicted that the tradeoff would impact internal consumer population characteristics, including biasing the stage structure towards adults, increasing adult size, and increasing average population‐level reproduction. This adult‐dominated stage structure was predicted to then lead to instability and a low quantity–high quality food state. Under all light levels, the manipulated populations became dominated by large adults. Contrary to predictions, the amplitudes of fluctuations in Daphnia biomass were lower in populations shifted to few–large offspring, representing higher stability in these populations. Furthermore, in high light conditions, a stable low Daphnia – high algae biomass (low food quality) state was observed in few–large offspring treatments but not in control (many–small offspring) treatments. Our results show a strong link between light levels as an extrinsic factor and the life‐history tradeoff of consumer offspring size versus number that impacts consumer–resource population dynamics through feedbacks with resource quality.     

Estimating Disease Prevalence Using Relatives of Case and Control Probands

Summary .  We introduce a method of estimating disease prevalence from case–control family study data. Case–control family studies are performed to investigate the familial aggregation of disease; families are sampled via either a case or a control proband, and the resulting data contain information on disease status and covariates for the probands and their relatives. Here, we introduce estimators for overall prevalence and for covariate-stratum-specific (e.g., sex-specific) prevalence. These estimators combine the proportion of affected relatives of control probands with the proportion of affected relatives of case probands and are designed to yield approximately unbiased estimates of their population counterparts under certain commonly made assumptions. We also introduce corresponding confidence intervals designed to have good coverage properties even for small prevalences. Next, we describe simulation experiments where our estimators and intervals were applied to case–control family data sampled from fictional populations with various levels of familial aggregation. At all aggregation levels, the resulting estimates varied closely and symmetrically around their population counterparts, and the resulting intervals had good coverage properties, even for small sample sizes. Finally, we discuss the assumptions required for our estimators to be approximately unbiased, highlighting situations where an alternative estimator based only on relatives of control probands may perform better.     

An organismal view of dendrochronology

An organism is the most basic unit of independent life. The tree-ring record is defined by organismal processes. Dendrochronology contributes to investigations far removed from organismal biology, e.g., archeology, climatology, disturbance ecology, etc. The increasing integration of dendrochronology into a diverse research community suggests an opportunity for a brief review of the organismal basis of tree rings.Trees are dynamic, competitive, and opportunistic organisms with diverse strategies for survival. As with all green plants, trees capture the energy in sunlight to make and break chemical bonds with the elements essential for life. These essential elements are taken from the atmosphere, water, and soil. The long tree-ring series of special interest to dendrochronology result from long-lived trees containing relatively little decayed wood. Both of those features result from organismal biology. While the tree-ring record tells us many things about local, regional, and even global environmental history, tree rings are first a record of tree survival.     

Short‐term Dynamics and the Effects of Biotic and Abiotic Factors on Plant Physiognomic Groups in a Hurricane‐impacted Lower Montane Tropical Forest

We assessed the short‐term effects of biotic (density, plant size) and abiotic factors (light), on the dynamics of physiognomically different plant groups (palms, tree ferns, lianas, and trees) in a hurricane‐impacted tropical wet montane forest, John Crow Mountains, Jamaica. All plants ≥2 cm (dbh) found within 45, 25 × 25 m permanent sample plots (2.8125 ha), established according to a randomized block design along an elevation gradient, were tagged and measured (dbh) in 2006 and re‐assessed in 2012 after Hurricane Dean (2007). Hemispheric light was measured in 2007 and 2008. Tree and liana size class distributions changed due to high mortality in the smallest size classes and their densities declined; however, palm and tree fern density remained unchanged. The dynamics of trees were only related to tree fern and liana dynamics (e.g., tree mortality was negatively related to liana recruitment etc.). Although pre‐ and posthurricane light was related to palm density and the density of the other plant groups, respectively, there were no significant changes in light. Tree survivorship increased with increasing dbh while posthurricane light and overall density influenced the growth and survivorship of tree species. Species importance value did not change, suggesting that direct regeneration may be the model of forest recovery following this small‐scale disturbance. Over the short term, tree species showed life history trade‐offs that aid species coexistence after this moderate/low disturbance event. Our study highlights that hurricanes with low impacts can have differential short‐ and possibly long‐term effects on different plant groups.     

Changes in leaf morphology and anatomy with tree age and height in the broadleaved evergreen species, Eucalyptus regnans F. Muell

Relatively little is known about changes in leaf attributes over the lifespan of woody plants. Knowledge of such changes may be useful in interpreting physiological changes with age. This study investigated changes in leaf morphology and anatomy with tree age and height in the broadleaved evergreen species, Eucalyptus regnans. Fully expanded leaves were sampled from the upper canopy of tree ages ranging from 6 to 240 years, and tree heights ranging from about 10–80 m. There were significant changes in leaf form with increasing tree age and height. Leaf size and specific leaf area (SLA; leaf area/leaf mass) decreased, leaf thickness increased, and leaves became narrower relative to their length, with increasing tree age and height. Cuticle thickness and leaf waxiness, including wax occlusion of the stomatal antechamber, increased with increasing age and height. By comparison, there were no clear trends in stomatal frequency or stomatal length with tree age, although there were curvilinear relationships between an index of total stomatal pore area per leaf lamina and both tree age and tree height. The results support the hypothesis that leaves of E. regnans become more xeromorphic with tree age and height. The results are discussed in relation to their significance for changes in water relations in the canopy with age.     

THE USE OF A MULTIPLE-TRANSFER METHOD IN PLANT VIRUS TRANSMISSION STUDIES—SOME STATISTICAL POINTS ARISING IN THE ANALYSIS OF RESULTS

The frequency of success of attempts to transmit a virus disease from one plant to another has long been used to measure the effects of any of the factors which influence transmission. Samples are taken from the population under test (e.g. vectors, diseased plants, etc.), and usually one sample is tested on each test plant; this is binomial sampling. However, in the procedure we name the 'multiple-transfer method' more than one sample may be tested on each test plant. This increases the number of samples tested without increasing the number of test plants used, and errors due to heterogeneity in the population under test are therefore minimized. Results from experiments using the multiple-transfer method may be evaluated by using the maximum likelihood estimator. The method is particularly reliable when the proportion of infected samples being studied is small, but can lead to considerable over-estimation when the proportion is high.     

Complex population dynamics and the coalescent under neutrality

Estimates of the coalescent effective population size N(e) can be poorly correlated with the true population size. The relationship between N(e) and the population size is sensitive to the way in which birth and death rates vary over time. The problem of inference is exacerbated when the mechanisms underlying population dynamics are complex and depend on many parameters. In instances where nonparametric estimators of N(e) such as the skyline struggle to reproduce the correct demographic history, model-based estimators that can draw on prior information about population size and growth rates may be more efficient. A coalescent model is developed for a large class of populations such that the demographic history is described by a deterministic nonlinear dynamical system of arbitrary dimension. This class of demographic model differs from those typically used in population genetics. Birth and death rates are not fixed, and no assumptions are made regarding the fraction of the population sampled. Furthermore, the population may be structured in such a way that gene copies reproduce both within and across demes. For this large class of models, it is shown how to derive the rate of coalescence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa, and how to simulate a coalescent tree conditional on a complex demographic history. This theoretical framework encapsulates many of the models used by ecologists and epidemiologists and should facilitate the integration of population genetics with the study of mathematical population dynamics.     

Responses of tree populations to climatic change

The influence of climate on the population dynamics of trees must be inferred from indirect sources of information because the long lifespans of trees preclude direct observation of population growth and decline. Important insights about these processes come from 1) observations of the life histories and ecologies of trees in contemporary forests, 2) evidence of recent treeline movements in remote areas unaffected by human disturbance, and 3) results of experiments performed on forest simulation models. Each line of evidence indicates that tree population responses are influenced by many factors: including lifespans, seed productivity and dispersibility, phenotypic plasticity, genetic variability, competition, and disturbance. Some population characteristics should allow rapid changes in population sizes, while others should confer stability in times of environmental fluctuation. Interactions between controlling factors should result in a wide array of possible responses to climatic change. Interpretations of late-Quaternary forest dynamics must be based on an understanding of the biological processes involved in population responses to environmental variations.     

Individual size variation and population stability in a seasonal environment: a discrete-time model and its calibration using grasshoppers

Much recent literature is concerned with how variation among individuals (e.g., variability in their traits and fates) translates into higher-level (i.e., population and community) dynamics. Although several theoretical frameworks have been devised to deal with the effects of individual variation on population dynamics, there are very few reports of empirically based estimates of the sign and magnitude of these effects. Here we describe an analytical model for size-dependent, seasonal life cycles and evaluate the effect of individual size variation on population dynamics and stability. We demonstrate that the effect of size variation on the population net reproductive rate varies in both magnitude and sign, depending on season length. We calibrate our model with field data on size- and density-dependent growth and survival of the generalist grasshopper Melanoplus femurrubrum. Under deterministic dynamics (fixed season length), size variation impairs population stability, given naturally occurring densities. However, in the stochastic case, where season length exhibits yearly fluctuations, size variation reduces the variance in population growth rates, thus enhancing stability. This occurs because the effect of size variation on net reproductive rate is dependent on season length. We discuss several limitations of the current model and outline possible routes for future model development.