Causal and Mechanistic Explanations in Ecology

How are scientific explanations possible in ecology, given that there do not appear to be many-if any-ecological laws? To answer this question, I present and defend an account of scientific causal explanation in which ecological generalizations are explanatory if they are invariant rather than lawlike. An invariant generalization continues to hold or be valid under a special change-called an intervention-that changes the value of its variables. According to this account, causes are difference-makers that can be intervened upon to manipulate or control their effects. I apply the account to ecological generalizations to show that invariance under interventions as a criterion of explanatory relevance provides interesting interpretations for the explanatory status of many ecological generalizations. Thus, I argue that there could be causal explanations in ecology by generalizations that are not, in a strict sense, laws. I also address the issue of mechanistic explanations in ecology by arguing that invariance and modularity constitute such explanations.     

The Potential of Genomic Approaches to Rotifer Ecology

Rotifers are a key component of many freshwater ecosystems, but surveys of the composition of rotifer communities are limited by the labor-intensiveness of sample processing, particularly of non-planktonic taxa, and by the shortage of investigators qualified to identify a broad range of rotifer species. Additional problems are posed by species that must be identified from living specimens, and by members of cryptic species complexes. As DNA sequencing becomes easier and cheaper, it has become practical to obtain representative DNA sequences from identified rotifer species for use in genome-based surveys to determine which rotifers are present in a new sample, avoiding the difficulties of traditional surveys. Here we discuss two genome-based tools used in surveys of microbial communities: serial analysis of gene tags (SAGT) and microarray hybridization. SAGT is a method for inexpensively obtaining characteristic short DNA sequences from a sample that can both identify taxa for which the tag sequence is known and signal the presence of additional uncharacterized species. Microarray hybridization allows detection of DNA sequences in the sample that are identical or similar to sequences present on the microarray. We also report the construction and hybridization of a small microarray of rotifer sequences, demonstrating that this method can discriminate among bdelloid families, and is likely to make much finer discriminations if appropriate sequences are present on the microarray. These techniques are most powerful when combined with traditional systematics in collaborative efforts, which may be fostered through the data base of rotifer biology, WheelBase (http://jbpc.mbl.edu/wheelbase).     

Integrating Thermal Physiology and Ecology of Ectotherms: A Discussion of Approaches

An understanding of interactions between the thermal physiologyand ecology of ectotherms remains elusive, partly because informationon the relative performance of whole-animal physiological systemsat ecologically relevant body temperatures is limited. Afterdiscussing physiological systems that have direct links to ecology(e.g., growth, locomotor ability), we review analytical methodsof describing and comparing certain aspects of performance (includingoptimal temperature range, thermal performance breadth), applythese techniques in an example on the thermal sensitivity oflocomotion in frogs, and evaluate potential applications.     

Introduction: From the New Ecology to the New Ecologies

An earlier ecological anthropology defined its project within the compass of the idealism v. materialism debate. Culture was an adaptive tool, instrumental rather than formal; it was intelligible with respect to its material effects, not—as the idealists would maintain—in terms of itself, as an autonomous, self-determining order of reality. This argument was mounted with respect to bounded, stable, self-regulating, local, or at best regional entities and the environment they inhabited. All of the premises of the earlier ecology have since been challenged, and today's ecologies—symbolic, historical, and political—radically depart from the reductions and elisions of the ecological anthropology of the past. In particular, the new ecologies override the dichotomies that informed and enlivened the debates of the past—nature/culture, idealism/materialism—and they are informed by the literature on transnationalist flows and local-global articulations. This introduction positions Rappaport's work within this historical shift from a polarized field of mutually exclusive frameworks to today's synthetic new ecologies and their antireductive materialism. Rappaport's work, produced over three decades, serves, in and through its own transformations, as a bridge between the reductive materialism of the past and a new-materialist ecology. [Rappaport, ecological anthropology, materialism v. idealism, the new materialism]     

Behavioural Ecology: Noise Annoys at Community Level

A new study on the impact of anthropogenic noise on birds takes a behavioural discipline to the level of community ecology: noise can not only harm individual species but also alter species relationships.     

微生物分子生态技术：16SrRNA／DNA方法

综述了以16SrRNA／DNA为基础的分子生物学技术在环境微生物种群分析中的应用,目的是使相关的科研人员能够对16SrRNA／DNA技术有一个比较完整的了解,并可以开展初步的实验工作。主要内容包括：DNA指纹技术、16rDNA文库的建立、DNA测序及微生物分类鉴定(即系统发育树分析)、基因探针设计和测试、荧光原位杂交和核酸印迹杂交等。     

Integrating Survey and Molecular Approaches to Better Understand Wildlife Disease Ecology

Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa) population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design) versus transmission (molecular case series study design) and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37–45%). The median Salmonella DICE coefficient (or Salmonella genetic similarity) was 52% (interquartile range [IQR]: 42–62%). Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density) determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is driven by local spatial, social, density and individual factors, rather than resources. This enhanced understanding has implications for the control of diseases in wildlife populations. Attempts to manage wildlife disease using simplistic density approaches do not acknowledge the complexity of disease ecology.     

植物群落学研究中整体论与个体论关系的探讨

分析了植物群落学研究中长期争论的整体性观点与个体性观点产生的历史背景和思想根源,并介绍了人们目前对二者关系的认识水平．由于植物群落既有整体性一面又有个体性的一面,指出今后植物群落学研究中应采取个体性与整体性相结合的方法以提高人们对复杂的植物群落的认识水平,更好地掌握其变化规律,以便设计更完美的人工生态系统．     

Ecological Theory and Community Restoration Ecology

Community ecological theory may play an important role in the development of a science of restoration ecology. Not only will the practice of restoration benefit from an increased focus on theory, but basic research in community ecology will also benefit. We pose several major thematic questions that are relevant to restoration from the perspective of community ecological theory and, for each, identify specific areas that are in critical need of further research to advance the science of restoration ecology. We ask, what are appropriate restoration endpoints from a community ecology perspective? The problem of measuring restoration at the community level, particularly given the high amount of variability inherent in most natural communities, is not easy, and may require a focus on restoration of community function (e.g., trophic structure) rather than a focus on the restoration of particular species. We ask, what are the benefits and limitations of using species composition or biodiversity measures as endpoints in restoration ecology? Since reestablishing all native species may rarely be possible, research is needed on the relationship between species richness and community stability of restored sites and on functional redundancy among species in regional colonist “pools.” Efforts targeted at restoring system function must take into account the role of individual species, particularly if some species play a disproportionate role in processing material or are strong interactors. We ask, is restoration of habitat a sufficient approach to reestablish species and function? Many untested assumptions concerning the relationship between physical habitat structure and restoration ecology are being made in practical restoration efforts. We need rigorous testing of these assumptions, particularly to determine how generally they apply to different taxa and habitats. We ask, to what extent can empirical and theoretical work on community succession and dispersal contribute to restoration ecology? We distinguish systems in which succession theory may be broadly applicable from those in which it is probably not. If community development is highly predictable, it may be feasible to manipulate natural succession processes to accelerate restoration. We close by stressing that the science of restoration ecology is so intertwined with basic ecological theory that practical restoration efforts should rely heavily on what is known from theoretical and empirical research on how communities develop and are structured over time.     

Gender and Risk in a Matrifocal Caribbean Community: A View from Behavioral Ecology

Matrifocality is a feature of Caribbean communities in which mothers and adult daughters often form the household core. I argue that daughter-biased parental care underlies matrifocality. Parental investment (PI) theory predicts sex-biased care, but factors promoting daughter preference are not always clearly specified. If sons are more likely than daughters to experience unpredictable hazards, then parents may bias their efforts toward daughters. In this study, I examine gender differences in rural Dominica and test PI predictions. Men were more likely to be poor and develop alcoholism and less likely to migrate or attend high school than women were. Educational outcomes showed a Trivers-Willard effect: Boys from unfavorable family environments were less likely to receive secondary education than were other boys, but there was no association for girls. PI variables generally accounted for less variance in men's outcomes than women's, suggesting that unpredictable hazards for sons may promote daughter preference and matrifocality.     

Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.     

New Approaches to Enzymatic Oligosaccharide Synthesis: Glycosynthases and Thioglycoligases

Abstract

An overview of the applications of engineered glycosynthases and thioglycoligases for the enzymatic synthesis of O- and S-glycosidic linkages in oligosaccharides is presented. Glycosynthases lack the catalytic nucleophile of retaining glycosidases and use glycosyl fluorides with inverted anomeric stereochemistry as glycosyl donors. To date, nine enzymes from seven different glycosyl hydrolase families have been engineered to perform the glycosynthase reaction. Thioglycoligases lack the catalytic acid/base residue of retaining glycosidases and use dinitrophenyl glycosides as donors and deoxy-thiosugars as acceptors. The regioselectivity of the transglycosylation reaction is entirely controlled by the position of the thiol in the acceptor. To date, two retaining exo glycosidases and one endo glycanase, all from different glycosyl hydrolase families, have been engineered in this fashion.     

Pathocenosis: A Holistic Approach to Disease Ecology

The History of medicine describes the emergence and recognition of infectious diseases, and human attempts to stem them. It also throws light on the role of changing environmental conditions on disease emergence/re-emergence, establishment and, sometimes, disappearance. However, the dynamics of infectious diseases is also influenced by the relationships between the community of interacting infectious agents present at a given time in a given territory, a concept that Mirko Grmek, an historian of medicine, conceptualized with the word “pathocenosis”. The spatial and temporal evolution of diseases, when observed at the appropriate scales, illustrates how a change in the pathocenosis, whether of “natural” or anthropic origin, can lead to the emergence and spread of diseases.     

Boranophosphate Oligonucleotides: New Synthetic Approaches

Abstract

Recently our laboratory reported a new backbone-modified class of oligonucleotides, with a borane (B₃3?) group replacing one of the non-bridging oxygen atoms. Here we present two new approaches to synthesize the boranophosphate oligonucleotides. All-stereoregular boranophosphate oligonucleotides can be prepared by enzymatic template extension reactions using nucleoside a-boranotriphosphates, which are good substrates for a number of polymerases. Larger scale synthesis of boranophosphate oligonucleotides can be carried out by effective chemical synthesis using the H-phosphonate approach, instead of previously used phosphoramidite methodology. The main advantage of H-phosphonate methodology is the ability to carry out one boronation reaction, after oligonucleotide chain elongation has been completed, using mild conditions without base damage and producing the desired boranophosphate oligonucleotides in high yield.