The effect of autocorrelation in environmental variability on the persistence of populations: an experimental test

Despite its significance regarding the conservation and management of biological resources, the body of theory predicting that the correlation between successive environmental states can profoundly influence extinction has not been empirically validated. Identical clonal populations from a model experimental system based on the collembolan Folsomia candida were used in the present study to investigate the effect of environmental autocorrelation on time to extinction. Environmental variation was imposed by variable implementation (present/absent) of a culling procedure according to treatments that represented six patterns of environmental autocorrelation. The average number of culling events was held constant across treatments but, as environmental autocorrelation increased, longer runs of both favourable and unfavourable culling tended to occur. While no difference was found among the survival functions for the various treatments, the time taken for 50% of the component populations to become extinct decreased significantly with increasing environmental autocorrelation. Similarly, analysis of all extinct populations demonstrated that time to extinction was shortened as environmental autocorrelation increased. However, this acceleration of extinction can be fully offset if sequential introduction is used in place of simultaneous introduction when founding the populations.     

An environmental perspective on metabolism

In principle the knowledge of an organism's metabolic network allows to infer its biosynthetic capabilities. Handorf et al. [2005. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 61, 498-512] developed a method of network expansion generating the set of all possible metabolites that can be produced from a set of compounds, given the structure of a metabolic network. Here we investigate the inverse problem: which chemical compounds or sets of compounds must be provided as external resources in order to sustain the growth or maintenance of an organism, given the structure of its metabolic network? Although this problem is highly combinatorial, we show that it is possible to calculate locally minimal nutrient sets that can be interpreted in terms of resource types. Using these types we predict broad nutritional requirements for 447 organisms, providing clues for possible environments from the knowledge of their metabolic networks.     

An ecological perspective on environmental decision-making

Current research on environmental decision-makers at the professional and nonprofessional levels is reviewed. The potential utility of this research for achieving more adaptive man-environment relations in modern industrial societies is examined. A broader framework of research is suggested for viewing the antecedents and consequences of environmental decision-making from an ecological perspective. Mechanisms for promoting research on man-environment relations are considered. In particular, issues in the training of scientific man-power in this interdisciplinary field are discussed.This article was prepared while the author served as Senior Postdoctoral Fellow in Environmental Psychology at Clark University, Worcester, Massachusetts, 1970–1971.     

An updated perspective on the polymerase division of labor during eukaryotic DNA replication

Abstract

In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.     

Towards genetic markers in animal populations as biomonitors for human-induced environmental change

Genetic markers provide potentially sensitive indicators of changes in environmental conditions because the genetic constitution of populations is normally altered well before populations become extinct. Genetic indicators in populations include overall genetic diversity, genetic changes in traits measured at the phenotypic level, and evolution at specific loci under selection. While overall genetic diversity has rarely been successfully related to environmental conditions, genetically based changes in traits have now been linked to the presence of toxins and both local and global temperature shifts. Candidate loci for monitoring stressors are emerging from information on how specific genes influence traits, and from screens of random loci across environmental gradients. Drosophila research suggests that chromosomal regions under recent intense selection can be identified from patterns of molecular variation and a high frequency of transposable element insertions. Allele frequency changes at candidate loci have been linked to pesticides, pollutants and climate change. Nevertheless, there are challenges in interpreting allele frequencies in populations, particularly when a large number of loci control a trait and when interactions between alleles influence trait expression. To meet these challenges, population samples should be collected for longitudinal studies, and experimental programmes should be undertaken to link variation at candidate genes to ecological processes.     

An updated review of environmental estrogen and androgen mimics and antagonists

For the last 40 y, substantial evidence has surfaced on the hormone-like effects of environmental chemicals such as pesticides and industrial chemicals in wildlife and humans. The endocrine and reproductive effects of these chemicals are believed to be due to their ability to: (1) mimic the effect of endogenous hormones, (2) antagonize the effect of endogenous hormones, (3) disrupt the synthesis and metabolism of endogenous hormones, and (4) disrupt the synthesis and metabolism of hormone receptors. The discovery of hormone-like activity of these chemicals occurred long after they were released into the environment. Aviation crop dusters handling DDT were found to have reduced sperm counts, and workers at a plant producing the insecticide kepone were reported to have lost their libido, became impotent and had low sperm counts. Subsequently, experiments conducted in lab animals demonstrated unambiguously the estrogenic activity of these pesticides. Man-made compounds used in the manufacture of plastics were accidentally found to be estrogenic because they fouled experiments conducted in laboratories studying natural estrogens. For example, polystyrene tubes released nonylphenol, and polycarbonate flasks released bisphenol-A. Alkylphenols are used in the synthesis of detergents (alkylphenol polyethoxylates) and as antioxidants. These detergents are not estrogenic; however, upon degradation during sewage treatment they may release estrogenic alkylphenols. The surfactant nonoxynol is used as intravaginal spermicide and condom lubricant. When administered to lab animals it is metabolized to free nonylphenol. Bisphenol-A was found to contaminate the contents of canned foods; these tin cans are lined with lacquers such as polycarbonate. Bisphenol-A is also used in dental sealants and composites. We found that this estrogen leaches from the treated teeth into saliva; up to 950 μg of bisphenol-A were retrieved from saliva collected during the first hour after polymerization. Other xenoestrogens recently identified among chemicals used in large volumes are the plastizicers benzylbutylphthalate, dibutylphthalate, the antioxidant butylhydroxyanisole, the rubber additive p-phenylphenol and the disinfectant o-phenylphenol. These compounds act cumulatively. In fact, feminized male fish were found near sewage outlets in several rivers in the U.K.; a mixture of chemicals including alkyl phenols resulting from degradation of detergents during sewage treatment seemed to be the causal agent. Estrogen mimics are just a class of endocrine disruptors. Recent studies identified antiandrogenic activity in environmental chemicals such as vinclozolin, a fungicide, and DDE, and insecticide. Moreover, a single chemical may produce neurotoxic, estrogenic and antiandrogenic effects. It has been hypothesized that endocrine disruptors may play a role in the decrease in the quantity and quality of human semen during the last 50 y, as well as in the increased incidence of testicular cancer and cryptorchidism in males and breast cancer incidence in both females and males in the industrialized word. To explore this hypothesis it is necessary to identify putative causal agents by the systematic screening of environmental chemicals and chemicals present in human foods to assess their ability to disrupt the endocrine system. In addition, it will be necessary to develop methods to measure cumulative exposure to (a) estrogen mimics, (b) antiandrogens, and (c) other disruptors.     

Demographic stochasticity and temporal autocorrelation in the dynamics of structured populations

Populations can show temporal autocorrelation in the dynamics arising from different mechanisms, including fluctuations in the demographic structure. This autocorrelation is often treated as a complicating factor in the analyses of stochastic population growth and extinction risk. However, it also reflects important information about the demographic structure. Here, we consider how temporal autocorrelation is related to demographic stochasticity in structured populations. Demographic stochasticity arises from inherent randomness in the demographic processes of individuals, like survival and reproduction, and the resulting impact on population growth is measured by the demographic variance. Earlier studies have shown that population structure have positive or negative effects on the demographic variance compared to a model where the structure is ignored. Here, we derive a new expression for the demographic variance of a structured population, using the temporal autocorrelation function of the population growth rate. We show that the relative difference in demographic variance when the structure is included or ignored (the effect of structure on demographic variance) is approximately twice the sum of the autocorrelations. We demonstrate the result for a simple hypothetical example, as well as a set of empirical examples using age‐structured models of 24 mammals from the demographic database COMADRE. In the empirical examples, the sum of the autocorrelation function was negative in all cases, indicating that age structure generally has a negative effect on the demographic variance (i.e. the demographic variance is lower compared to that of a model where the structure is ignored). Other kinds of structure, such as spatial heterogeneity affecting fecundity, can have positive effects on the demographic variance, and the sum of the autocorrelations will then be positive. These results yield new insights into the complex interplay between population structure, demographic variance, and temporal autocorrelation, that shapes the population dynamics and extinction risk of populations.     

Testing environmental and genetic effects in the presence of spatial autocorrelation

Spatial autocorrelation is a well‐recognized concern for observational data in general, and more specifically for spatial data in ecology. Generalized linear mixed models (GLMMs) with spatially autocorrelated random effects are a potential general framework for handling these spatial correlations. However, as the result of statistical and practical issues, such GLMMs have been fitted through the undocumented use of procedures based on penalized quasi‐likelihood approximations (PQL), and under restrictive models of spatial correlation. Alternatively, they are often neglected in favor of simpler but more questionable approaches. In this work we aim to provide practical and validated means of inference under spatial GLMMs, that overcome these limitations. For this purpose, a new software is developed to fit spatial GLMMs. We use it to assess the performance of likelihood ratio tests for fixed effects under spatial autocorrelation, based on Laplace or PQL approximations of the likelihood. Expectedly, the Laplace approximation performs generally slightly better, although a variant of PQL was better in the binary case. We show that a previous implementation of PQL methods in the R language, glmmPQL, is not appropriate for such applications. Finally, we illustrate the efficiency of a bootstrap procedure for correcting the small sample bias of the tests, which applies also to non‐spatial models.     

Epigenetics in natural animal populations

Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally‐mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.     

Mathematical studies in animal populations

Zusammenfassung Die vorliegende Arbeit ist eine Fortsetzung derThompson'schen Analysen des Parasitenzyklus bei Insekten, die mit der irrealen Folgerung endeten, dass unter gewissen Voraussetzungen — die wir in der gegenwärtigen Analyse akzeptiert haben —jeder Parasit in relativ kurzer Generationenfolge seinen Wirt, und damit sich selbst, zur Ausrottung bringen muss. Der Einfluss von wiederkehrenden Umwelt-katastrophen wie sie z.B. durch ungünstiges Wetter sehr häufig bedingt sind, wurde untersucht mit dem Ergebnis, dass solche Katastrophen, wenn sie in nicht allzugrossen Intervallen auftreten, völlig genügen, um die Unterbrechung der akkumulativen Parasitierung im Zyklus zu erklären.Die grössere Empfindlichkeit der Parasiten, welche aus allen Beobachtungen und Analysen sich ergibt, ist nicht physiologisch, sondern ökologisch bedingt. Methodisch hat sich gezeigt, dass die Analyse tierischer Populationen weitgehend ohne Anwendung von Integralen möglich ist.Die Ergebnisse, welche die hohe Bedeutung der Feinde bei grosser Wirtsdichte, und ihre minimale Wirksamkeit, wenn letztere niedrig ist, zeigen, sind unabhängig von einem besonderen Dichtefaktor der Feindvermehrung — wie er im allgemeinen besteht und die aufgezeigten Tendenzen noch verstärkt — gewonnen. Der Einfluss des Superparasiten wird unter dem Einfluss wiederkehrender Umwelt-katastrophen minimal. Am Modell einiger beobachteter Gradationen wird die Übereinstimmung mit unserer Analvse demonstriert.

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Résumé Le travail ci-dessus est la continuation des analyses deThompson des cycles parasitaires chez les insectes, qui l'ont à la conclusion absurde qu'en acceptant certaines suppositions — que nous avons acceptées dans la présente analyse — chaque parasite exterminerait son hôte et par conséquent soi-même. Nous avons étudié l'influence de certains phénomènes catastrophiques récurrents provenant du milieu comme par exemple celle d'un temps défavorable. Ces phénomènes, pourvu qu'ils ne se présentent pas à des intervalles trop grands, suffisent amplement pour expliquer l'interruption de la parasitation accumulative dans les cycles.La sensibilité plus grande des parasites qui est démontrée dans toutes les observations et analyses ne provient pas de causes physiologiques, mais écologiques.La méthodologie a donné comme résultat intéressant le fait que l'analyse des populations animales peut se faire sans l'application des intégrales.Les résultats démontrant la grande importance des ennemis quand les hôtes sont nombreux, mais par contre une activité minimale des ennemis quand les hôtes sont rares, ont été obtenus indépendamment d'une augmentation spéciale des ennemis qui, en général, constitue un facteur important, ce qui renforce encore les tendances que nous avons trouvées. L'influence des superparasites devient minime sous l'action des catastrophes récurrentes dus au milieu. Finalement, au moyen de quelques gradations bien observées, nous avons démontré que notre analyse est conforme aux faits.

     

An everlasting role of animal models in understanding human disease

<正>Model organisms have been widely used to dissect important biological phenomena, as well as to explore potential causes and treatments for human disorders. Much of our knowledge on molecular mechanisms underlying the heredity, development as well as physiology is largely derived from the researches of model organisms. We have witnessed     

The statistical implications of autocorrelation for detection in environmental health assessment

Many environmental health and risk assessment techniques and models aim at estimating the fluctuations of selected biological endpoints through the time domain as a means of assessing changes in the environment or the probability of a particular measurement level occurring. In either case, estimates of the sample variance and mean of the sample variance are crucial to making appropriate statistical inferences. The commonly employed statistical techniques for estimating both measures presume the data were generated by a covariance stationary process. In such cases, the observations are treated as independently and identically distributed and classical statistical testing methods are applied. However, if the assumption of covariance stationarity is violated, the resulting sample variance and variance of the sample mean estimates are biased. The bias compromises statistical testing procedures by increasing the probability of detecting significance in tests of mean and variance differences. This can lead to inappropriate decisions being made about the severity of environmental damage. Accordingly, it is argued that data sets be examined for correlation in the time domain and appropriate adjustments be made to the required estimators before they are used in statistical hypothesis testing. Only then can credible and scientifically defensible decisions be made by environmental decision makers and regulators.     

Chicken domestication: an updated perspective based on mitochondrial genomes

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A–I and W–Z. Common haplogroups A–G were shared by domestic chickens and red junglefowl. Rare haplogroups H–I and W–Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.     

An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations

We examined long-term surveillance data on antimicrobial resistance (AMR) in Salmonella Typhimurium DT104 (DT104) isolates from concurrently sampled and sympatric human and animal populations in Scotland. Using novel ecological and epidemiological approaches to examine diversity, and phenotypic and temporal relatedness of the resistance profiles, we assessed the more probable source of resistance of these two populations. The ecological diversity of AMR phenotypes was significantly greater in human isolates than in animal isolates, at the resolution of both sample and population. Of 5200 isolates, there were 65 resistance phenotypes, 13 unique to animals, 30 unique to humans and 22 were common to both. Of these 22, 11 were identified first in the human isolates, whereas only five were identified first in the animal isolates. We conclude that, while ecologically connected, animals and humans have distinguishable DT104 communities, differing in prevalence, linkage and diversity. Furthermore, we infer that the sympatric animal population is unlikely to be the major source of resistance diversity for humans. This suggests that current policy emphasis on restricting antimicrobial use in domestic animals may be overly simplistic. While these conclusions pertain to DT104 in Scotland, this approach could be applied to AMR in other bacteria-host ecosystems.     

Evaluating spatial autocorrelation and depletion in pitfall-trap studies of environmental gradients

Studies of environmental gradients like edge effects commonly employ designs where samples are collected at unequal distances within transects. This approach risks confounding species patterns caused by the environmental gradient with patterns resulting from the spatial arrangement of the sampling scheme. Spatial autocorrelation and depletion (reduced catch) have the potential to influence pitfall-trap collections of invertebrates. Readily available control data from a study of edge and riparian effects on forest litter beetles was used to assess autocorrelation and depletion effects. Data from control transects distant from the treatment transects located at habitat edges and streams were screened to determine whether the study design (pitfall traps at varying distances within transects) was imposing patterns on the data attributable to differential autocorrelation or depletion. Autocorrelation in species composition and assemblage structure was not detected within the 99 m transects. The abundance and species richness of beetles were not lower where traps were in closer proximity, indicating that the transect design was not causing measurable depletion or resulting in differential trap catch. These findings indicate that spatial autocorrelation and depletion are unlikely to impair further analyses of edge and riparian effects on litter beetles.