分子生物学方法在环境微生物生态学中的应用研究进展

随着分子生物学方法的不断发展和改进,微生物在生态系统中的作用被更好的挖掘出来。目前快速发展的先进的分子生物学技术,已经开始应用于分析环境微生物的多样性、微生物的生物地理学及微生物对气候变化的响应等。一般环境微生物的研究目标主要有3个,即确定微生物的种类和多样性、微生物的功能或潜在作用及在特定时间点活跃的微生物等。然而,现有微生物的研究方法复杂多样,容易给研究者在方法的选择上带来困惑。将从微生物的多样性和功能研究两个方面介绍和分析相应的分子生物学方法,尤其是近年来快速发展的高通量测序、宏组学和单细胞水平研究方法(如纳米二次离子质谱与荧光原位杂交相结合的方法)等新技术及其应用情况,以期为研究者选择合适的研究方法进行环境微生物的研究提供依据。     

Integrating molecular genetics and ecology in studies of adaptive radiation: whitefish, Coregonus sp., as a case study

Species pairs of whitefish (Coregonus sp.) found in postglacial lakes are used to illustrate the benefits of combining molecular and ecological approaches in studies of adaptive radiation. A detailed mitochondrial DNA phylogeographic analysis revealed that this species complex is composed of five major phylogenetic groups identifying races that survived the Pleistocene glaciations in distinct refugia. It also provided evidence for parallel evolution of sympatric ecotypes, involving bofh allopatric and sympatric origins. This strongly indicated the role of natural selection in driving their divergence. A comparative analysis of niche partitioning supported the hypothesis that the persistence of differential ecological opportunity throughout their ontogeny may be the selective force promoting the extent of specialization reached by whitefish ecotypes. The possibility that these same ecological processes are also responsible for determining the extent of their reproductive isolation was supported by a negative correlation between the extent of gene flow, estimated from microsatellite loci, and that of morphological specialization between ecotypes in different lakes. Previous experimental studies, however, revealed that embryonic mortality rates were 2 to 5 times higher in hybrid compared to pure crosses of ecotypes from distinct glacial races. This indicates that both genetic and ecological mechanisms may jointly act to determine speciation rate in whitefish. It is hoped that this study will not only stimulate further the interest of evolutionary ecologists for molecular genetics, but also that of molecularists for ecology. Promoting the fusion of such apparentiy remote fields of research may represent the most important achievement of molecular ecology as a discipline.     

Scientific personae in American psychology: three case studies

This paper studies the constellations of attitudes--sentimental, moral, epistemological, and social--that three leading psychologists active in turn-of-the-twentieth-century America took to be essential to the production of scientific knowledge. William James, G. Stanley Hall, and Edward Titchener located the virtues and traits proper to the scientific frame of mind, and combined them into normative images of the man of science, or, 'scientific personae' as I use the term here. I argue that their competing formulations of the scientific ethos informed their psychological practice and epistemological commitments. James, Hall, and Titchener mobilized their representations of the man of science in order to reconfigure the field of psychology and redefine its boundaries, as well as to promote forms of sociability and define the proper role of scientists both within the academy and in the wider polity.     

The role of replication studies in ecology

Recent large‐scale projects in other disciplines have shown that results often fail to replicate when studies are repeated. The conditions contributing to this problem are also present in ecology, but there have not been any equivalent replication projects. Here, we survey ecologists' understanding of and opinions about replication studies. The majority of ecologists in our sample considered replication studies to be important (97%), not prevalent enough (91%), worth funding even given limited resources (61%), and suitable for publication in all journals (62%). However, there is a disconnect between this enthusiasm and the prevalence of direct replication studies in the literature which is much lower (0.023%: Kelly 2019) than our participants' median estimate of 10%. This may be explained by the obstacles our participants identified including the difficulty of conducting replication studies and of funding and publishing them. We conclude by offering suggestions for how replications could be better integrated into ecological research.     

Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles

Although still controversial, estimation of divergence times using molecular data has emerged as a powerful tool to examine the tempo and mode of evolutionary change. Two primary obstacles in improving the accuracy of molecular dating are heterogeneity in DNA substitution rates and accuracy of the fossil record as calibration points. Recent methodological advances have provided powerful methods that estimate relative divergence times in the face of heterogeneity of nucleotide substitution rates among lineages. However, relatively little attention has focused on the accuracy of fossil calibration points that allow one to translate relative divergence times into absolute time. We present a new cross-validation method that identifies inconsistent fossils when multiple fossil calibrations are available for a clade and apply our method to a molecular phylogeny of living turtles with fossil calibration times for 17 of the 22 internal nodes in the tree. Our cross-validation procedure identified seven inconsistent fossils. Using the consistent fossils as calibration points, we found that despite their overall antiquity as a lineage, the most species-rich clades of turtles diversified well within the Cenozoic. Many of the truly ancient lineages of turtles are currently represented by a few, often endangered species that deserve high priority as conservation targets.     

The effect of molecular inhibition on evolutionary learning: studies in the hypernetwork architecture

The hypernetwork architecture is a biologically inspired learning model based on abstract molecules and molecular interactions that exhibits functional and organizational correlation with biological systems. Hypernetwork organisms were trained, by molecular evolution, to solve N-input parity tasks. We found that learning improves when molecules exhibit inhibitory sites, allowing molecular inhibition and opening the possibility of forming negative feedback regulatory pathways. Optimal learning is achieved when at least 20% of the molecules in each cell have inhibitory sites. Intra-cellular as well as inter-cellular molecular inhibitions play an important role in the information processing of hypernetwork organisms, by maintaining a balance of the molecular cascade reactions. Similar mechanisms inside neurons are considered important for memory.     

The molecular revolution in ectomycorrhizal ecology: peeking into the black-box

Molecular tools have now been applied for the past 5 years to dissect ectomycorrhizal (EM) community structure, and they have propelled a resurgence in interest in the field. Results from these studies have revealed that: (i) EM communities are impressively diverse and are patchily distributed at a fine scale below ground; (ii) there is a poor correspondence between fungi that appear dominant as sporocarps vs. those that appear dominant on roots; (iii) members of Russulaceae, Thelephoraceae, and/or non-thelephoroid resupinates are among the most abundant EM taxa in ecosystems sampled to date; (iv) dissimilar plants are associated with many of the same EM species when their roots intermingle--this occurs on a small enough spatial scale that fungal individuals are likely to be shared by dissimilar plants; and (v) mycoheterotrophic plants have highly specific fungal associations. Although, these results have been impressive, they have been tempered by sampling difficulties and limited by the taxonomic resolution of restriction fragment length polymorphism methods. Minor modifications of the sampling schemes, and more use of direct sequencing, has the potential to solve these problems. Use of additional methods, such as in situ hybridization to ribosomal RNA or hybridization coupled to microarrays, are necessary to open up the analysis of the mycelial component of community structure.     

The case for developmental ecology

We call for renewed emphasis on the tasks confronting animals as they develop and learn. We are extending the use of the term ‘developmental ecology’ employed by plant biologists who have studied how fitness can be influenced by the ecological context present during development (Watson et al. 2001, Evolutionary Ecology,15, 425-442). We seek an expanded venue for the term, arguing that for animal behaviourists to understand some of the traits so familiar in behavioural ecology, they must consider the fundamental phenomena of development. Not doing so runs the risk of misidentifying both the proximal and functional causes of traits. For example, without a developmental view, macrogeographical variation in species-typical behaviour may be viewed as evidence of genotypic differences when, in fact, the variation is being produced by developmental contexts. Detailed below are some general issues about how development can be studied if it is to contribute to our knowledge of the adaptive value of behavioural systems. We argue for a prospective and longitudinal orientation, with an emphasis on relatively continuous observation and measurement. Both behaviours and contexts that may only occur during ontogeny are examined, as well as the reproductive outcome of the traits of interest. We present examples from our work on courtship and communication in brown-headed cowbirds, Molothrus ater, to show that a prospective and ecological view of development reveals pronounced variation in patterns of reproductive behaviour that cannot be understood without taking into account developmental ecology.     

Genetic tagging: contemporary molecular ecology

Population genetic analyses have been highly successful in deciphering inter- and intra-specific evolutionary relationships, levels of gene flow, genetic divergence and effective population sizes. Parameters estimated by traditional population genetic analyses are evolutionary averages and thus not necessarily relevant for contemporary ecological or conservation issues. Molecular data can, however, also provide insight into contemporary patterns of divergence, population size and gene flow when a sufficient number of variable loci are analysed to focus subsequent data analyses on individuals rather than populations. Genetic tagging of individuals is an example of such individual-based approaches and recent studies have shown it to be a viable alternative to traditional tagging methods. Owing to the ubiquitous presence of hyper-variable DNA sequences in eukaryote genomes it is in principle possible to tag any eukaryote species and the required DNA can be obtained indirectly from substrates such as faeces, sloughed skin and hair. The purpose of this paper is to present the concept of genetic tagging and to further advocate the extension of individual-based genetic analyses beyond the identification of individuals to other kinds of relationships, such as parent-offspring relations, which more fully exploit the genetic nature of the data.     

Measuring temporal patterns in ecology: The case of mast seeding

1. Properly assessing temporal patterns is a central issue in ecology in order to understand ecosystem processes and their mechanisms. Mast seeding has traditionally been described as a reproductive behavior consisting of highly variable and synchronized reproductive events. The most common metric used to measure temporal variability and thus infer masting behavior, the coefficient of variation (CV), however, has been repeatedly suggested to improperly estimate temporal variability. Biases of CV estimates are especially problematic for non‐normally distributed data and/or data sets with a high number of zeros.
2. Some recent studies have already adopted new metrics to measure temporal variability, but most continue to use CV. This controversy has started a strong debate about what metrics to use.
3. We here summarize the problems of CV when assessing temporal variability, particularly across data sets containing a large number of zeros, and highlight the benefits of using other metrics of temporal variability, such as proportional variability (PV) and consecutive disparity (D). We also suggest a new way to look at reproductive behavior, by separating temporal variability from frequency of reproduction, to allow better comparison of data sets with different characteristics.
4. We suggest future studies to properly describe the temporal patterns in fully scientific and measurable terms that do not lead to confusion, such as variability and frequency of reproduction, using robust and fully comparable metrics.

     

Molecular ecology of fungal entomopathogens: molecular genetic tools and their applications in population and fate studies

The power of molecular genetic techniques to address ecological research questions has opened a distinct interdisciplinary research area collectively referred to as molecular ecology. Molecular ecology combines aspects of diverse research fields like population and evolutionary genetics, as well as biodiversity, conservation biology, behavioural ecology, or species-habitat interactions. Molecular techniques detect specific DNA sequence characteristics that are used as genetic markers to discriminate individuals or taxonomic groups, for instance in analyses of population and community structures, for elucidation of phylogenetic relationships, or for the characterization and monitoring of specific strains in the environment. Here, we summarize the PCR-based molecular techniques used in molecular ecological research on fungal entomopathogens and discuss novel techniques that may have relevance to the studies of entomopathogenic fungi in the future. We discuss the flow chart of the molecular ecology approaches and we highlight some of the critical steps involved. There are still many unresolved questions in the understanding of the ecology of fungal entomopathogens. These include population characteristics and relations of genotypes and habitats as well as host-pathogen interactions. Molecular tools can provide substantial support for ecological research and offer insight into this far inaccessible systems. Application of molecular ecology approaches will stimulate and accelerate new research in the field of entomophathogen ecology.     

Didactics of molecular ecology

Summary Molecular biology conferred enormous progresses in biosciences during the past few years. This paradigm permutation in biological research certainly challenges biological education. Nevertheless, this is no reason to fundamentally reorganise biological education at the universities. A most entire view of the matter should remain a central request which meets the capacity and imagination of students. Selected biological phenomena taken from the traditional treasury remain suitable in the future too to mediate basic biological ways ot thinking. Forthcoming syllabuses, however, will necessitate the expansion of this concept. The scope of the present contribution is to show, how the integration of molecular biology in the teaching of classical disciplines of biology may be reached. Choosing ecology and environmental biology as examples, molecular biology will not only strengthen explanation models of cause-effect relationships in these disciplines, but also will facilitate the interconnections to interdisciplinary fields such as health education, social, and political education. This may result in an entire structural concept of classical and molecular biology.     

生态学研究的新领域--分子生态学

分子生态是生态学的一个新的研究领域。它采用分子生物学的技术与方法来研究生态活动规律的分子机理。本文简要介绍了分子生态学的定义、研究内容、研究方法和研究热点等,以期描述出分子生态学的概貌。