Organisational closure in biological organisms

The central aim of this paper consists in arguing that biological organisms realize a specific kind of causal regime that we call "organisational closure"; i.e., a distinct level of causation, operating in addition to physical laws, generated by the action of material structures acting as constraints. We argue that organisational closure constitutes a fundamental property of biological systems since even its minimal instances are likely to possess at least some of the typical features of biological organisation as exhibited by more complex organisms. Yet, while being a necessary condition for biological organization, organisational closure underdetermines, as such, the whole set of requirements that a system has to satisfy in order to be taken as a paradigmatic example of organism. As we suggest, additional properties, as modular templates and control mechanisms via dynamical decoupling between constraints, are required to get the complexity typical of full-fledged biological organisms.     

Conflicting demands on wetland ecosystem services: nutrient retention,biodiversity or both?

1. Wetland ecosystems may, besides having considerable economical value, increase landscape biodiversity and function as traps for nutrients from land to freshwater‐ and marine systems. As a result of these features, wetlands are nowadays often protected and restored, and many countries have even initiated wetland construction programmes. 2. In the present study, we aim at increasing the knowledge on how to improve the design of a wetland with respect to both biodiversity and nutrient retention, by analysing physical, chemical and biological features of a large set of constructed wetlands. 3. Our results show that a combination of the wetland features, namely shallow depth, large surface area and high shoreline complexity are likely to provide a high biodiversity of birds, benthic invertebrates and macrophytes and to have high nitrogen retention, whereas a small, deep wetland is likely to be more efficient in phosphorus retention, but less valuable in terms of biodiversity. 4. Hence, among the features used to design new wetlands, area, depth and shoreline complexity have fundamental, and sometimes conflicting, effects on nutrient retention and biodiversity. This means that there are, within limits, possibilities to direct the ecosystem function of a specific wetland in desired directions.     

Gould on Laws in Biological Science

Are there laws in evolutionary biology? Stephen J. Gould has argued that there are factors unique to biological theorizing which prevent the formulation of laws in biology, in contradistinction to the case in physics and chemistry. Gould offers the problem of ’’complexity‘‘ as just such a fundamental barrier to biological laws in general, and to Dollo‘s Law in particular. But I argue that Gould fails to demonstrate: (1) that Dollo‘s Law is not law-like, (2) that the alleged failure of Dollo‘s Law demonstrates why there cannot be laws in biological science, and (3) that ’’complexity‘‘ is a fundamental barrier to nomologicality.     

Towards a resolution of ‘the paradox of the plankton’: A brief overview of the proposed mechanisms

In plankton ecology, it is a fundamental question as to how a large number of competing phytoplankton species coexist in marine ecosystems under a seemingly-limited variety of resources. This ever-green question was first proposed by Hutchinson [Hutchinson, G.E., 1961. The paradox of the plankton. Am. Nat. 95, 137–145] as ‘the paradox of the plankton’. Starting from Hutchinson [Hutchinson, G.E., 1961. The paradox of the plankton. Am. Nat. 95, 137–145], over more than four decades several investigators have put forward varieties of mechanisms for the extreme diversity of phytoplankton species. In this article, within the boundary of our knowledge, we review the literature of the proposed solutions and give a brief overview of the mechanisms proposed so far. The proposed mechanisms that we discuss mainly include spatial and temporal heterogeneity in physical and biological environment, externally imposed or self-generated spatial segregation, horizontal mesoscale turbulence of ocean characterized by coherent vortices, oscillation and chaos generated by several internal and external causes, stable coexistence and compensatory dynamics under fluctuating temperature in resource competition, and finally the role of toxin-producing phytoplankton in maintaining the coexistence and biodiversity of the overall plankton population that we have proposed recently. We find that, although the different mechanisms proposed so far is potentially applicable to specific ecosystems, a universally accepted theory for explaining plankton diversity in natural waters is still an unachieved goal.     

Selecting networks of nature reserves: methods do affect the long-term outcome

Data on vascular plants of boreal lakes in Finland were used to compare the efficiency of reserve selection methods in representing four aspects of biodiversity over a 63 year period. These aspects included species richness, phylogenetic diversity, restricted range diversity and threatened species. Our results show that the efficiency of reserve selection methods depends on the selection criteria used and on the aspect of biodiversity under consideration. Heuristic methods and optimizing algorithms were nearly equally efficient in selecting lake networks over a small geographical range. In addition, a scoring procedure was observed to be efficient in maintaining different aspects of biodiversity over time. However, the random selection of lakes seems to be the most inefficient option for a reserve network. In general, reserve selection methods seem to favour lakes that maximize one aspect of diversity at the time of selection, but the network may not be the best option for maintaining the maximum diversity over time. The reserve selection methods do affect the long-term outcome but it is impossible to recommend one method over the others unequivocally.     

Characterising and predicting benthic biodiversity for conservation planning in deepwater environments

Understanding patterns of biodiversity in deep sea systems is increasingly important because human activities are extending further into these areas. However, obtaining data is difficult, limiting the ability of science to inform management decisions. We have used three different methods of quantifying biodiversity to describe patterns of biodiversity in an area that includes two marine reserves in deep water off southern Australia. We used biological data collected during a recent survey, combined with extensive physical data to model, predict and map three different attributes of biodiversity: distributions of common species, beta diversity and rank abundance distributions (RAD). The distribution of each of eight common species was unique, although all the species respond to a depth-correlated physical gradient. Changes in composition (beta diversity) were large, even between sites with very similar environmental conditions. Composition at any one site was highly uncertain, and the suite of species changed dramatically both across and down slope. In contrast, the distributions of the RAD components of biodiversity (community abundance, richness, and evenness) were relatively smooth across the study area, suggesting that assemblage structure (i.e. the distribution of abundances of species) is limited, irrespective of species composition. Seamounts had similar biodiversity based on metrics of species presence, beta diversity, total abundance, richness and evenness to the adjacent continental slope in the same depth ranges. These analyses suggest that conservation objectives need to clearly identify which aspects of biodiversity are valued, and employ an appropriate suite of methods to address these aspects, to ensure that conservation goals are met.     

Introduction and establishment processes of marine species: a study case with the Japanese brown kelp Undaria pinnatifida

The number of biological introductions has increased since the 1970's and is now considered as the second major cause of the biodiversity erosion, after fragmentation or disappearance of habitat. Beyond the threat they represent for the ecosystem equilibrium, introduced species are interesting models to study fundamental issues in ecology and evolution like the processes of dispersal and adaptation to novel environments. In this context, species introduced over a large geographic range and spectrum of habitats provide an excellent opportunity for comparing the mechanisms that promote introduction and settlement between different environments. In this paper, based on a case study, the worldwide introduction of the brown alga Undaria pinnatifida, and on the use of molecular tools, we aim at examining several processes promoting or occurring during biological introductions. Our results showed that i) multiple processes can account for the success of the pandemic introduction of this alga, highlighting the necessity to study introduced species in relation with the ecosystem they invaded, ii) the recurrence of introductions is a critical component in the dynamics of settlement and iii) human activities can play a major role not only during the primary introduction but also for the sustainable settlement of introduced species in natural environments by providing reservoir of migrants. Taken together, these results demonstrate that the complexity of mechanisms occurring in biological invasion require spatial but also long-term analysis.     

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species’ abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth’s Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth’s biodiversity.

This study describes a novel mechanistic engine that predicts a realistic global latitudinal diversity gradient, species richness distribution and phylogenies. This approach is a step towards the interdisciplinary numeric understanding of the physical and biological processes that have shaped Earth’s biodiversity.     

植物化感作用与生物多样性

本文简要地阐释了化感作用的含义、基本特征以及作用机制,并结合生物多样性理论,综述了化感作用研究中化感物种的多样性、化感物质的多样性及其释放途径的多样性,具体讨论了化感作用对物种多样性、遗传多样性及生态系统多样性中的种群生态、协同进化、土壤生境、生态系统功能和生物入侵等方面的可能影响。文中提出了化感作用的利用、管理应与生物多样性保护相统一的看法,并指出对化感作用与生物多样性的关系以及相互影响机制进行本质的探索,特别是对植物化感作用的生态服务功能与价值评估与探讨,可为保护生物学和系统生态学提供理论基础,这也是今后工作开展的一个重要方向。     

Demonstration of a satellite-based index to monitor habitat at continental-scales

An important initial step in the conservation and sustainable management of the Earth's biodiversity is to implement systems to both identify and subsequently monitor components of biological diversity, along with developing a better understanding of the processes that significantly threaten their conservation or sustainable use. Key factors in both species diversity and richness are related to environmental heterogeneity which is driven by temporal and spatial variation in the biological, physical, and chemical features of the environment. These environmental characteristics are manifest through the condition and change in vegetation productivity (considered as an integrated response of vegetation to climate and soil conditions). Earth observation is uniquely capable of synoptically covering large areas of the planet in a repeatable, and cost effective manner, and is a well-established technology for detecting terrestrial vegetation productivity. A recently developed dynamic habitat index (DHI), based on satellite observations of the fraction of radiation absorbed by the canopy (fPAR), has been shown to effectively cluster remotely sensed observations into a range of habitat regimes which in turn have been related to breeding bird surveys in the Canadian Province of Ontario and across the conterminous United States. With evidence that the index is well correlated with species diversity, we consider, in this subsequent paper, whether such an index is a suitable candidate as a continental index to characterize and subsequently monitor habitat conditions. To do so, we first utilise available fPAR data available from 2000 to 2005 over North America, and apply the index. Using information on continental terrestrial ecozones and their ecological distinctiveness, we then compare and contrast the index and utilize trajectory analysis to assess what changes have occurred in the index over the 6-year time period and possible implications for continental biodiversity. The potential application of the index is the discussed.     

Establishing the evidence base for maintaining biodiversity and ecosystem function in the oil palm landscapes of South East Asia

The conversion of natural forest to oil palm plantation is a major current threat to the conservation of biodiversity in South East Asia. Most animal taxa decrease in both species richness and abundance on conversion of forest to oil palm, and there is usually a severe loss of forest species. The extent of loss varies significantly across both different taxa and different microhabitats within the oil palm habitat. The principal driver of this loss in diversity is probably the biological and physical simplification of the habitat, but there is little direct evidence for this. The conservation of forest species requires the preservation of large reserves of intact forest, but we must not lose sight of the importance of conserving biodiversity and ecosystem processes within the oil palm habitat itself. We urgently need to carry out research that will establish whether maintaining diversity supports economically and ecologically important processes. There is some evidence that both landscape and local complexity can have positive impacts on biodiversity in the oil palm habitat. By intelligent manipulation of habitat complexity, it could be possible to enhance not only the number of species that can live in oil palm plantations but also their contribution to the healthy functioning of this exceptionally important and widespread landscape.     

Hyperbolic growth of marine and continental biodiversity through the phanerozoic and community evolution

Among diverse models that are used to describe and interpret the changes in global biodiversity through the Phanerozoic, the exponential and logistic models (traditionally used in population biology) are the most popular. As we have recently demonstrated (Markov, Korotayev, 2007), the growth of the Phanerozoic marine biodiversity at genus level correlates better with the hyperbolic model (widely used in demography and macrosociology). Here we show that the hyperbolic model is also applicable to the Phanerozoic continental biota at genus and family levels, and to the marine biota at species, genus, and family levels. There are many common features in the evolutionary dynamics of the marine and continental biotas that imply similarity and common nature of the factors and mechanisms underlying the hyperbolic growth. Both marine and continental biotas are characterized by continuous growth of the mean longevity of taxa, by decreasing extinction and origination rates, by similar pattern of replacement of dominant groups, by stepwise accumulation of evolutionary stable, adaptable and "physiologically buffered" taxa with effective mechanisms of parental care, protection of early developmental stages, etc. At the beginning of the development of continental biota, the observed taxonomic diversity was substantially lower than that predicted by the hyperbolic model. We suggest that this is due, firstly, to the fact that, during the earliest stages of the continental biota evolution, the groups that are not preserved in the fossil record (such as soil bacteria, unicellular algae, lichens, etc.) played a fundamental role, and secondly, to the fact that the continental biota initially formed as a marginal portion of the marine biota, rather than a separate system. The hyperbolic dynamics is most prominent when both marine and continental biotas are considered together. This fact can be interpreted as a proof of the integrated nature of the biosphere. In the macrosociological models, the hyperbolic pattern of the world population growth arises from a non-linear second-order positive feedback between the demographic growth and technological development (more people - more potential inventors - faster technological growth - the carrying capacity of the Earth grows faster - faster population growth - more people - more potential inventors, and so on). Based on the analogy with macrosociological models and diverse paleontological data, we suggest that the hyperbolic character of biodiversity growth can be similarly accounted for by a non-linear second-order positive feedback between the diversity growth and community structure complexity. The feedback can work via two parallel mechanisms: 1) decreasing extinction rate (more taxa- higher alpha diversity, or mean number of taxa in a community - communities become more complex and stable - extinction rate decreases - more taxa, and so on) and 2) increasing origination rate (new taxa facilitate niche construction; newly formed niches can be occupied by the next "generation" of taxa). The latter possibility makes the mechanisms underlying the hyperbolic growth of biodiversity and human population even more similar, because the total ecospace of the biota is analogous to the "carrying capacity of the Earth" in demography. As far as new species can increase ecospace and facilitate opportunities for additional species entering the community, they are analogous to the "inventors" of the demographic models whose inventions increase the carrying capacity of the Earth. The hyperbolic growth of the Phanerozoic biodiverstiy suggests that "cooperative" interactions between taxa can play an important role in evolution, along with generally accepted competitive interactions. Due to this "cooperation", the evolution of biodiversity acquires some features of a self-accelerating process. Macroevolutionary "cooperation" reveals itself in: 1) increasing stability of communities that arises from alpha diversity growth; 2) ability of species to facilitate opportunities for additional species entering the community.     

Inferring the Dynamics of Diversification: A Coalescent Approach

Recent analyses of the fossil record and molecular phylogenies suggest that there are fundamental limits to biodiversity, possibly arising from constraints in the availability of space, resources, or ecological niches. Under this hypothesis, speciation rates decay over time and biodiversity eventually saturates, with new species emerging only when others are driven to extinction. This view of macro-evolution contradicts an alternative hypothesis that biodiversity is unbounded, with species ever accumulating as they find new niches to occupy. These contrasting theories of biodiversity dynamics yield fundamentally different explanations for the disparity in species richness across taxa and regions. Here, we test whether speciation rates have decayed or remained constant over time, and whether biodiversity is saturated or still expanding. We first derive a general likelihood expression for internode distances in a phylogeny, based on the well-known coalescent process from population genetics. This expression accounts for either time-constant or time-variable rates, time-constant or time-variable diversity, and completely or incompletely sampled phylogenies. We then compare the performance of different diversification scenarios in explaining a set of 289 phylogenies representing amphibians, arthropods, birds, mammals, mollusks, and flowering plants. Our results indicate that speciation rates typically decay over time, but that diversity is still expanding at present. The evidence for expanding-diversity models suggests that an upper limit to biodiversity has not yet been reached, or that no such limit exists.     

Relationships between biodiversity and biological control in agroecosystems: Current status and future challenges

Agricultural systems around the world are faced with the challenge of providing for the demands of a growing human population. To meet this demand, agricultural systems have intensified to produce more crops per unit area at the expense of greater inputs. Agricultural intensification, while yielding more crops, generally has detrimental impacts on biodiversity. However, intensified agricultural systems often have fewer pests than more “environmentally-friendly” systems, which is believed to be primarily due to extensive pesticide use on intensive farms. In turn, to be competitive, less-intensive agricultural systems must rely on biological control of pests. Biological pest control is a complex ecosystem service that is generally positively associated with biodiversity of natural enemy guilds. Yet, we still have a limited understanding of the relationships between biodiversity and biological control in agroecosystems, and the mechanisms underlying these relationships. Here, we review the effects of agricultural intensification on the diversity of natural enemy communities attacking arthropod pests and weeds. We next discuss how biodiversity of these communities impacts pest control, and the mechanisms underlying these effects. We focus in particular on novel conceptual issues such as relationships between richness, evenness, abundance, and pest control. Moreover, we discuss novel experimental approaches that can be used to explore the relationships between biodiversity and biological control in agroecosystems. In particular, we highlight new experimental frontiers regarding evenness, realistic manipulations of biodiversity, and functional and genetic diversity. Management shifts that aim to conserve diversity while suppressing both insect and weed pests will help growers to face future challenges. Moreover, a greater understanding of the interactions between diversity components, and the mechanisms underlying biodiversity effects, would improve efforts to strengthen biological control in agroecosystems.     

Biodiversity: negotiating the border between nature and culture

In a context of globalization, Article 8j. from the Convention on Biological Diversity recognizes the value of biodiversity and formalizes its mixed nature through its biological as well as cultural dimensions. This new definition raises questions more than it solves them. We demonstrate that national and international organizations, local communities, and even researchers from different disciplines (anthropology, botany or genetics) identify and evaluate biodiversity differently. The various stakeholder groups have developed an unavoidable social relation with multiple aspects of biodiversity that they relate to through their job or way of life. And therefore, they pursue various conservation purposes: the preservation of place’s memory through ancestral links, cultural diversity, phenotypic variability or evolutionary potential. Which disciplinary and ethical boundaries are these actors willing to compromise, in order to preserve biodiversity in the name of development? Which indicators should we choose to fulfil which goals? The contrasting examples of taro (a socially valued object, planted on taro pondfields inherited “from the ancestors”, linked to an important cultural diversity and to a narrow genetic-base) and coconut (a socially devalued object, cultivated in coconut plantations at the prompting of “the Whites” and genetically diverse despite few named types) demonstrate that same farmers from a village in Vanuatu (South Pacific) affirm traditional ecological knowledge though their management of taro, and still participate in a market economy by intensifying their crop of coconuts. Conservation and research programs should integrate ethical questions and political processes to reconcile systems of diversified values and representations.     

Deep-sea nematode biodiversity in the Mediterranean basin: testing for longitudinal, bathymetric and energetic gradients

The knowledge of the processes controlling the spatial distribution of species diversity is one of the main challenges of the present ecological research. Spatial patterns of benthic biodiversity in the deep sea are poorly known in comparison with other ecosystems and this limits our understanding of the mechanisms controlling the distribution and maintenance of high biodiversity in the largest ecosystems of our biosphere. Although the Mediterranean basin covers <1% of the world ocean surface, none the less it hosts >7.5% of the global biodiversity. The high biogeographic complexity and the presence of steep ecological gradients contribute in making the Mediterranean a region of very high diversity. Here we report the results of an investigation on the patterns of nematode biodiversity in the deep-Mediterranean Sea, in relation with bathymetric, longitudinal and energetic gradients. Our results indicate that benthic biodiversity in the deep-Mediterranean decreases significantly with increasing depth. Moreover, at equally deep sites, nematode diversity decreased from the western to the eastern basin and longitudinal gradients were evident when comparing sites at 4000-m depth, with 3000-m depth. The analysis of the available energy (measured as labile organic matter content of the sediments) suggests that biodiversity patterns are not controlled by the amounts of food resources, but instead bio-availability is the key factor. A more detailed analysis revealed an extremely high deep-sea beta-diversity (turnover diversity), both among sites at different depths as well as at similar depths of different longitude or within the same basin. This new finding has not only important implications on the estimates of the overall regional diversity (gamma diversity), but also suggests the presence of high biogeographic complexity in the deep benthic domain of the Mediterranean Sea.     

Macroinvertebrate community composition and diversity in ephemeral and perennial ponds on unregulated floodplain meadows in the UK

Ponds are common and abundant landscape features in temperate environments, particularly on floodplains where lateral connectivity with riverine systems persists. Despite their widespread occurrence and importance to regional diversity, research on the ecology and hydrology of temperate ephemeral and perennial floodplain ponds lags behind that of other shallow waterbodies. This study examines the aquatic macroinvertebrate diversity of 34 ponds (20 perennial and 14 ephemeral) on two unregulated riverine floodplain meadows in Leicestershire, UK. Perennial ponds supported nearly twice the diversity of ephemeral ponds. Despite frequent inundation of floodwater and connectivity with other floodplain waterbodies, ephemeral ponds supported distinct invertebrate communities when compared to perennial ponds. When the relative importance of physical, chemical, biological and spatial characteristics was examined, physical and chemical characteristics were found to account for more variation in community composition than biological or spatial variables. The results suggest that niche characteristics rather than neutral colonisation processes dominate the structure of invertebrate communities of floodplain ponds. The maintenance of pond networks with varying hydroperiod lengths and environmental characteristics should be encouraged as part of conservation management strategies to provide heterogeneous environmental conditions to support and enhance aquatic biodiversity at a landscape scale.