Analysis of biodiversity across levels of biological organization: a problem of defining traits

Biodiversity is a term that comprises the appearance, structure and function of all levels of biological organization, including genes, species and ecosystems. The vast majority of measures of biodiversity (usually termed ‘diversity indices’) considers only number, proportion and distribution of species which belong to a specified group and exist in a defined area or ecosystem. Genetic diversity as a part of biodiversity within species (or populations) was either not regarded in this respect or was treated (by geneticists) as a separate entity of diversity quantified with separate measures. Little attention has been given to the integration of both types of diversity, within and among species, in a single measurement (termed ‘transspecific’ diversity). In order to attain this integration on a general basis, an operational trait concept is developed which allows the determination of variation in traits observable in members not only of the same species but also of different species. The concept rests on methods of investigation that can be adapted to a broader range of organisms without modification of their characteristics. Once a trait is specified on this basis, any meaningful measure of diversity can be applied to assess biodiversity across levels of biological organization. The utility of the concept is demonstrated by application to the results of an earlier study on associations between species and genetic diversity in a forest tree community. Attributes of isozymes which are visible in electrophoresis are used as a transspecific genetic trait.     

Levels of understanding in ecology: interspecific competition and community ecology

Abstract Ecological interpretation has been subject to several divisive controversies, involving, for example, the significance of density dependence and interspecific competition as ecological processes. Generally, resolution has been obtained through compromise and concensus or calls for yet more data. Essentially, both sides in the discussion are seen to have been correct to some extent. As a consequence the debates have been portrayed widely as having been sterile. We agree, but only because they have been conducted at a level so superficial that the relevance of the original criticisms to the theoretical structure of ecology has not been widely appreciated, nor resolved. Debate that deals with ecological generalizations must be conducted at a level appropriate to such aims.     

A new system for understanding the biodiversity in different nature reserves:capacity,connectivity and quality of biodiversity

In this paper,we propose a new system for understanding the biodiversity in different conservation areas.It includes three aspects:the capacity,the connectivity and the quality.The capacity refers to the numbers of biodiversity,including absolute and relative richness of the vegetation types Nv and Dv = (Nv-1)/lnA,species numbers S and richness of species dGI = (S- 1)/lnA,and germ plasm resources within a nature reserve,and also the potential biological living space offered by the natural resource.It comprises the total biological resources in a nature reserve.The connectivity refers to the flux of biodiversity,including similarity and connected status of the vegetation types SILi = 2z/(x + y) and species numbers SIc = 2z/(x + y) among different nature reserves.The quality refers to the stability of biodiversity,including relative species richness index RSLi = d/dmax,relative vegetation richness index RVLi =Dv/Dmaxv,fastness to invasion species fLi = 1-Si/St,weighted values,representativeness and vulnerability of special vegetations,special species,CITES species and rare species as the protected targets.     

A new system for understanding the biodiversity in different nature reserves: capacity, connectivity and quality of biodiversity

In this paper, we propose a new system for understanding the biodiversity in different conservation areas. It includes three aspects: the capacity, the connectivity and the quality. The capacity refers to the numbers of biodiversity, including absolute and relative richness of the vegetation types N _v and D _v =(N _v −1)/lnA, species numbers S and richness of species d _Gl =(S − 1)/lnA, and germ plasm resources within a nature reserve, and also the potential biological living space offered by the natural resource. It comprises the total biological resources in a nature reserve. The connectivity refers to the flux of biodiversity, including similarity and connected status of the vegetation types SI _Li =2z/(x + y) and species numbers SI _C =2z/(x + y) among different nature reserves. The quality refers to the stability of biodiversity, including relative species richness index RS _Li =d/d _max, relative vegetation richness index RV _Li =D _v /D _maxv , fastness to invasion species ƒ _Li =1−S _i /S _t , weighted values, representativeness and vulnerability of special vegetations, special species, CITES species and rare species as the protected targets.     

Drosophila bristles and the nature of quantitative genetic variation

Numbers of Drosophila sensory bristles present an ideal model system to elucidate the genetic basis of variation for quantitative traits. Here, we review recent evidence that the genetic architecture of variation for bristle numbers is surprisingly complex. A substantial fraction of the Drosophila genome affects bristle number, indicating pervasive pleiotropy of genes that affect quantitative traits. Further, a large number of loci, often with sex- and environment-specific effects that are also conditional on background genotype, affect natural variation in bristle number. Despite this complexity, an understanding of the molecular basis of natural variation in bristle number is emerging from linkage disequilibrium mapping studies of individual candidate genes that affect the development of sensory bristles. We show that there is naturally segregating genetic variance for environmental plasticity of abdominal and sternopleural bristle number. For abdominal bristle number this variance can be attributed in part to an abnormal abdomen-like phenotype that resembles the phenotype of mutants defective in catecholamine biosynthesis. Dopa decarboxylase (Ddc) encodes the enzyme that catalyses the final step in the synthesis of dopamine, a major Drosophila catecholamine and neurotransmitter. We found that molecular polymorphisms at Ddc are indeed associated with variation in environmental plasticity of abdominal bristle number.     

Linking community and disease ecology: the impact of biodiversity on pathogen transmission

The increasing number of zoonotic diseases spilling over from a range of wild animal species represents a particular concern for public health, especially in light of the current dramatic trend of biodiversity loss. To understand the ecology of these multi-host pathogens and their response to environmental degradation and species extinctions, it is necessary to develop a theoretical framework that takes into account realistic community assemblages. Here, we present a multi-host species epidemiological model that includes empirically determined patterns of diversity and composition derived from community ecology studies. We use this framework to study the interaction between wildlife diversity and directly transmitted pathogen dynamics. First, we demonstrate that variability in community composition does not affect significantly the intensity of pathogen transmission. We also show that the consequences of community diversity can differentially impact the prevalence of pathogens and the number of infectious individuals. Finally, we show that ecological interactions among host species have a weaker influence on pathogen circulation than inter-species transmission rates. We conclude that integration of a community perspective to study wildlife pathogens is crucial, especially in the context of understanding and predicting infectious disease emergence events.     

The confusion between scale-defined levels and conventional levels of organization in ecology

Abstract. Conventional levels of organization in ecology can be hierarchically ordered, but there is not necessarily a time or space scale-dependent difference between the classes: cell, organism, population, community, ecosystem, landscape, biome and biosphere. The physical processes that ecological systems must obey are strictly scaled in time and space, but communities or ecosystems may be either large or small. Conventional levels of organization are not scale-dependent, but are criteria for telling foreground from background, or the object from its context. We erect a scheme that separates scale-ordered levels from the conventional levels of organization. By comparing landscapes, communities and ecosystems all at the same scale, we find that communities and ecosystems do not map onto places on the landscape. Rather, communities and ecosystems are wave interference patterns between processes and organisms interfering with and accomodating to each other, even though they occur at different scales on the landscape, and so have different periodicities in their waved behavior. Population members are usually commensurately scaled and so do not generally interact to give interference patterns. Populations are therefore tangible, oratleastcan be assigned a location at an instant in time.     

Natural genetic variation as a tool in understanding the role of CETP in lipid levels and disease

Since the identification of cholesteryl ester transfer protein (CETP), its role in the modulation of HDL levels and cardiovascular disease has been debated. With the early detection of genetic variants followed by the finding of families deficient in CETP, genetic studies have played a large role in the attempts to understand the association of CETP with lipids and disease; however, results of these studies have often led to disparate conclusions. With the availability of a greater variety of genetic polymorphisms and larger studies in which disease has been examined, it is now possible to compare the breadth of CETP genetic studies and draw better conclusions. The most broadly studied polymorphism is TaqIB for which over 10,000 individuals have been genotyped and had HDL levels determined. When these studies are subjected to a meta-analysis, the B2B2 homozygotes are found to have higher HDL levels than B1B1 homozygotes (0.12 mmol/l, 95% CI = 0.11-0.13, P < 0.0001). A similar analysis of the I405V polymorphism yields 0.05 mmol/l higher HDL levels in 405VV homozygotes than in 405II homozygotes (95% CI = 0.03-0.07, P < 0.0001). The implications of these studies for cardiovascular disease will be addressed.     

Applying population and community ecology theory to advance understanding of belowground biogeochemistry

Approaches to quantifying and predicting soil biogeochemical cycles mostly consider microbial biomass and community composition as products of the abiotic environment. Current numerical approaches then primarily emphasise the importance of microbe–environment interactions and physiology as controls on biogeochemical cycles. Decidedly less attention has been paid to understanding control exerted by community dynamics and biotic interactions. Yet a rich literature of theoretical and empirical contributions highlights the importance of considering how variation in microbial population ecology, especially biotic interactions, is related to variation in key biogeochemical processes like soil carbon formation. We demonstrate how a population and community ecology perspective can be used to (1) understand the impact of microbial communities on biogeochemical cycles and (2) reframe current theory and models to include more detailed microbial ecology. Through a series of simulations we illustrate how density dependence and key biotic interactions, such as competition and predation, can determine the degree to which microbes regulate soil biogeochemical cycles. The ecological perspective and model simulations we present lay the foundation for developing empirical research and complementary models that explore the diversity of ecological mechanisms that operate in microbial communities to regulate biogeochemical processes.     

Evolutionary ecology and the conservation of biodiversity

Studies on evolving interactions among species and the coevolutionary process have suggested that the conservation of biodiversity requires a broad geographic perspective, if the `interaction biodiversity' of the earth is to be conserved with its species diversity. Continued maintenance of the geographic mosaic of specialization, defense and population structure appears to be crucial to the coevolutionary process and the long-term persistence of some interspecific interactions.     

From genes to ecosystems: a synthesis of the effects of plant genetic factors across levels of organization

Using two genetic approaches and seven different plant systems, we present findings from a meta-analysis examining the strength of the effects of plant genetic introgression and genotypic diversity across individual, community and ecosystem levels with the goal of synthesizing the patterns to date. We found that (i) the strength of plant genetic effects can be quite high; however, the overall strength of genetic effects on most response variables declined as the levels of organization increased. (ii) Plant genetic effects varied such that introgression had a greater impact on individual phenotypes than extended effects on arthropods or microbes/fungi. By contrast, the greatest effects of genotypic diversity were on arthropods. (iii) Plant genetic effects were greater on above-ground versus below-ground processes, but there was no difference between terrestrial and aquatic environments. (iv) The strength of the effects of intraspecific genotypic diversity tended to be weaker than interspecific genetic introgression. (v) Although genetic effects generally decline across levels of organization, in some cases they do not, suggesting that specific organisms and/or processes may respond more than others to underlying genetic variation. Because patterns in the overall impacts of introgression and genotypic diversity were generally consistent across diverse study systems and consistent with theoretical expectations, these results provide generality for understanding the extended consequences of plant genetic variation across levels of organization, with evolutionary implications.     

Consequences of variation in plant defense for biodiversity at higher trophic levels

Antagonistic interactions between insect herbivores and plants impose selection on plants to defend themselves against these attackers. Although selection on plant defense traits has typically been studied for pairwise plant-attacker interactions, other community members of plant-based food webs are unavoidably affected by these traits as well. A plant trait might, for example, affect parasitoids and predators feeding on the herbivore. Consequently, defensive plant traits structure the diversity and composition of the complex community associated with the plant, and communities as a whole also feed back to selection on plant traits. Here, we review recent developments in our understanding of how plant defense traits structure insect communities and discuss how molecular mechanisms might drive community-wide effects.     

Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology

The pace of on‐going climate change calls for reliable plant biodiversity scenarios. Traditional dynamic vegetation models use plant functional types that are summarized to such an extent that they become meaningless for biodiversity scenarios. Hybrid dynamic vegetation models of intermediate complexity (hybrid‐DVMs) have recently been developed to address this issue. These models, at the crossroads between phenomenological and process‐based models, are able to involve an intermediate number of well‐chosen plant functional groups (PFGs). The challenge is to build meaningful PFGs that are representative of plant biodiversity, and consistent with the parameters and processes of hybrid‐DVMs. Here, we propose and test a framework based on few selected traits to define a limited number of PFGs, which are both representative of the diversity (functional and taxonomic) of the flora in the Ecrins National Park, and adapted to hybrid‐DVMs. This new classification scheme, together with recent advances in vegetation modeling, constitutes a step forward for mechanistic biodiversity modeling.     

Evolutionary genetics: the nature of hidden genetic variation unveiled

It has long been known that wild-type phenotypes harbor considerable amounts of ‘hidden’ genetic variation. A new study has mapped this variation at the nucleotide level and revealed some unexpected properties.     

Interactions between temperature and nutrients across levels of ecological organization

Temperature and nutrient availability play key roles in controlling the pathways and rates at which energy and materials move through ecosystems. These factors have also changed dramatically on Earth over the past century as human activities have intensified. Although significant effort has been devoted to understanding the role of temperature and nutrients in isolation, less is known about how these two factors interact to influence ecological processes. Recent advances in ecological stoichiometry and metabolic ecology provide a useful framework for making progress in this area, but conceptual synthesis and review are needed to help catalyze additional research. Here, we examine known and potential interactions between temperature and nutrients from a variety of physiological, community, and ecosystem perspectives. We first review patterns at the level of the individual, focusing on four traits – growth, respiration, body size, and elemental content – that should theoretically govern how temperature and nutrients interact to influence higher levels of biological organization. We next explore the interactive effects of temperature and nutrients on populations, communities, and food webs by synthesizing information related to community size spectra, biomass distributions, and elemental composition. We use metabolic theory to make predictions about how population‐level secondary production should respond to interactions between temperature and resource supply, setting up qualitative predictions about the flows of energy and materials through metazoan food webs. Last, we examine how temperature–nutrient interactions influence processes at the whole‐ecosystem level, focusing on apparent vs. intrinsic activation energies of ecosystem processes, how to represent temperature–nutrient interactions in ecosystem models, and patterns with respect to nutrient uptake and organic matter decomposition. We conclude that a better understanding of interactions between temperature and nutrients will be critical for developing realistic predictions about ecological responses to multiple, simultaneous drivers of global change, including climate warming and elevated nutrient supply.