Biodiversity Governance: A Tower of Babel of Scales and Cultures

The recently created Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), originally focused on multilateral and global issues, is shifting its focus to address local issues and to include in its assessments local stakeholders and indigenous and traditional systems of knowledge. Acknowledging that full biodiversity governance is unavoidably rooted in participation of local actors and their problems and knowledge, we suggest that to deal successfully with the complexity and diversity of local issues, including indigenous knowledge systems, IPBES must recognize a key role of local institutions.     

The end of the microarray Tower of Babel: will universal standards lead the way?

Microarrays are the most common method of studying global gene expression, and may soon enter the realm of FDA-approved clinical/diagnostic testing of cancer and other diseases. However, the acceptance of array data has been made difficult by the proliferation of widely different array platforms with gene probes ranging in size from 25 bases (oligonucleotides) to several kilobases (complementary DNAs or cDNAs). The algorithms applied for image and data analysis are also as varied as the microarray platforms, perhaps more so. In addition, there is a total lack of universally accepted standards for use among the different platforms and even within the same array types. Due to this lack of coherency in array technologies, confusion in interpretation of data within and across platforms has often been the norm, and studies of the same biological phenomena have, in many cases, led to contradictory results. In this commentary/review, some of the causes of this confusion will be summarized, and progress in overcoming these obstacles will be described, with the goal of providing an optimistic view of the future for the use of array technologies in global expression profiling and other applications.     

Rethinking ecological inference: density dependence in reef fishes

We use a meta‐analysis of density dependence in reef fishes to evaluate how ecologists approach detection, inference, and estimation. We compared two groups of studies: those that detected effects of density on survival and those that did not. Distinctions between these groups have spawned heated debate about the processes that affect fish dynamics. Per capita effects of density were similar between the two groups, although total effects (and hence ambient density) were greater in studies that detected density effects. The majority of the variation in effects of density was not resolved by the classification of studies based on the authors' conclusions. These results suggest (1) that standard inferences based on null hypothesis tests may miss important sources of variation in effects and give rise to unnecessary debate; and (2) that estimation of effect sizes and model parameters (including their uncertainty) is a powerful alternative to detection of ecological processes.     

Density and ecological importance of bacteria on kelp fronds in an upwelling region

Bacteria on the surfaces of fronds of two co-occurring species of kelp have been sampled at monthly intervals for a year in the Benguela upwelling region. Counts of viable bacteria were obtained by the spread plate technique. Bacterial counts at frond bases of both kelps followed a seasonal pattern with minima of 10³ cells·cm^?2 in winter and maxima of 10⁶ cells·cm^?2 in late summer, similar to the bacterio-plankton cycle. At frond tips bacterial densities remained high (≈ 10⁷ cells·cm²) throughout the year and were significantly denser than on other parts of the frond. There was no significant difference between kelp species. Rate of frond erosion does not vary significantly at different seasons, and a minimal estimate of average daily contribution of bacteria eroding off frond tips with the tissue is 2.6 × 10⁹ cells·m^?2·day^?1. The large standing stock of benthic suspension-feeding animals probably utilizes this nitrogen-rich resource.     

Density dependence in cereal aphid populations

Long sequences of data on the incidence of cereal aphids from five European countries were analysed for evidence of density dependent processes occurring between years. Using a randomisation test (Pollard, Lakhani & Rotheray, 1987), density dependence was revealed in all (16) population censuses of Metopolo-phium dirhodum , 60% of Rhopalosiphum padi censuses (10 of 17) but only 25% of Sitobion avenae population censuses (4 of 16). Correcting for density independent effects of weather revealed the existence of significant direct density dependence in some populations censuses where it was previously undetected. The implications of density dependence in cereal aphid populations are considered.     

Density dependence and the stabilization of animal numbers

Summary The claim of Varley and Gradwell that the highly density-dependent pupal predation (k₅) in the population of the winter moth in Wytham Wood, England would keep density within limits (regulate) is compared in this paper with the density limits in the null model: pupal predation causes the same mean generation mortality (35%) as in the field, but is not density-dependent, i.e. either constant or randomly fluctuating between years according to the actual frequency distribution, ceteris paribus. According to this null model the winter moth would have fluctuated between narrower limits than in the field; the claim of Varley & Gradwell must thus be rejected. It is more generally concluded that a regulating factor should be the key factor, but this is not a sufficient condition. It should also prevent in some way the low throughs in the time series that usually accompany the operation of a dominating density-dependent mortality factor.Communication No. 264 of the Biological Station, Wijster     

Density dependence and the stabilization of animal numbers

Summary Latto and Hassell (1987) disagree with the conclusion of Den Boer (1986), that the winter moth population at Wytham Wood, studied by Varley and Gradwell, was not regulated. They attempt to demonstrate regulation by means of a simulation model. In the present paper the validity of this model is tested step by step. The fixing of the initial and final densities, as practised by Den Boer and rejected by Latto and Hassell, did not prevent population explosions and extinctions, as was assumed by Latto and Hassell. It is shown that the deterministic formulation of the density dependence of pupal predation, as used by Latto and Hassell, deviates systematically from the field data. Replacing the values of the key-factor (k₁) by random values drawn from a normal distribution (Latto and Hassell) affects the dynamics such that the ability of pupal predation to govern density is improved in the model. Changing mortalities other than the key-factor does not significantly influence the pattern of fluctuations nor the limits of density. Models should leave intact the essentials of the reality under study, while removing distracting elements (Levins 1968). As both the timing of the key-factor, and its correlation with pupal predation are essential features of the winter moth population at Wytham Wood between 1950 and 1968, the model of Latto and Hassell does not apply to this population. By simply changing log₁₀ (eggs/female) it is shown that the power of the density dependence of pupal predation to govern possible trends in density of the winter moth population at Wytham Wood is weak. On the other hand, the model of Latto and Hassell gives insight into the conditions that might favour regulation of numbers. Although the model of Poethke and Kirchberg (1987) preserves more features of the pertinent winter moth population than that of Latto and Hassell (1987) it still deviates in one essential aspect: the succession in time of both the (coupled) mortalities and the deviations from the deterministic density dependence are taken at random. Therefore, also this model is still too far from the field population to be a sound base for the statistical speculation proposed by Poethke and Kirchberg.Communication No. 339 of the Biological Station, Wijster     

Density dependence and the control of helminth parasites

1. The transient dynamics and stability of a population are determined by the interplay between species density, its spatial distribution and the positive and negative density-dependent processes regulating population growth. 2. Using the human-helminth parasite system as an example, we propose that the life-stage upon which negative density dependence operates will influence the rate of host reinfection following anthelmintic chemotherapy, and the likely success of control programmes. 3. Simple deterministic models are developed which highlight how a parasite species whose population size is down-regulated by density-dependent establishment will reinfect a host population at a faster rate than a species with density-dependent parasite fecundity. 4. Different forms of density dependence can produce the same equilibrium behaviour but different transient dynamics. Under-representing the nature and magnitude of density-dependent mechanisms, and in particular those operating upon establishing life-stages, may cause the resilience of the parasite population to a control perturbation to be underestimated.     

Density dependence hypotheses and the distribution of fecundity

1. Beja & Palma (2008, Journal of Animal Ecology, 77, doi: 10.1111/j.1365-2656.2007.01312.x) attempt to provide a critical analysis of the effectiveness and limitations of a previously published method (Ferrer et al. 2006, Journal of Animal Ecology, 75, 111-117.) to discriminate between Habitat Heterogeneity Hypothesis and the Individual Adjustment Hypothesis using real data from a Bonelli's eagle Hieraaetus fasciatus population. 2. They conclude that significant and strong correlations between mean and CV or skewness are expected under a biologically plausible assumption about brood size distribution, and that the two hypotheses cannot therefore be distinguished. 3. A major concern we have with their paper centres on this biologically plausible brood-size distribution. They used the same quasi-Poisson distribution of brood sizes (typical for a saturate population under Habitat Heterogeneity Hypothesis) for both families of simulations. So, is not surprising that both groups gave similar results. 4. They argued that this approach was 'empirical', free of theoretical assumptions. But in testing between hypotheses, what we are looking for is precisely the differences among theoretical brood-size distributions predicted under the two hypotheses. 5. Summarizing, with the same mean fecundity at high densities, both hypotheses must have different brood-size distributions. So the use of a single left-skewed distribution, typical of a real saturated population (most likely under Habitat Heterogeneity Hypothesis) in attempts to distinguish between the two hypotheses by re-sampling several times on the same left-skewed distribution, as done by Beja & Palma, is clearly inappropriate.     

Density dependence triggers runaway selection of reduced senescence

In the presence of exogenous mortality risks, future reproduction by an individual is worth less than present reproduction to its fitness. Senescent aging thus results inevitably from transferring net fertility into younger ages. Some long-lived organisms appear to defy theory, however, presenting negligible senescence (e.g., hydra) and extended lifespans (e.g., Bristlecone Pine). Here, we investigate the possibility that the onset of vitality loss can be delayed indefinitely, even accepting the abundant evidence that reproduction is intrinsically costly to survival. For an environment with constant hazard, we establish that natural selection itself contributes to increasing density-dependent recruitment losses. We then develop a generalized model of accelerating vitality loss for analyzing fitness optima as a tradeoff between compression and spread in the age profile of net fertility. Across a realistic spectrum of senescent age profiles, density regulation of recruitment can trigger runaway selection for ever-reducing senescence. This novel prediction applies without requirement for special life-history characteristics such as indeterminate somatic growth or increasing fecundity with age. The evolution of nonsenescence from senescence is robust to the presence of exogenous adult mortality, which tends instead to increase the age-independent component of vitality loss. We simulate examples of runaway selection leading to negligible senescence and even intrinsic immortality.     

Density dependence in resource exploitation: empirical test of Levins' metapopulation model

Levins' model of metapopulation dynamics is modified to incorporate variable degrees of density dependence in the per capita exploitation of resource patches. We demonstrate a simple means of testing for this density dependence in a sample of metapopulations, each at its equilibrium balance of local colonization to extinction. The fraction of habitable unoccupied patches equilibrates to a constant number under the null model of density independent colonization, and to a constant proportion under strong density dependence. We compare the null model to two density dependent alternatives, using data on exploitation of nest boxes by collared flycatchers Ficedula albicollis . The analysis shows how predicted trends in the equilibrium unoccupied fraction are similar for both spatial interference and net immigration. This needs to be recognized, since the null hypothesis of a constant unused resource applies also to the dynamics of consumable resources, where it is expressed in a constant stock of uneaten prey at the dynamic equilibrium of predators to prey.     

Protist taxonomy: an ecological perspective

This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems.     

Mammalian reproduction: an ecological perspective

The objectives of this paper are to organize our concepts about the environmental regulation of reproduction in mammals and to delineate important gaps in our knowledge of this subject. The environmental factors of major importance for mammalian reproduction are food availability, ambient temperature, rainfall, the day/night cycle and a variety of social cues. The synthesis offered here uses as its core the bioenergetic control of reproduction. Thus, for example, annual patterns of breeding are viewed as reflecting primarily the caloric costs of the female's reproductive effort as they relate to the energetic costs and gains associated with her foraging effort. Body size of the female is an important consideration since it is correlated with both potential fat reserves and life span. Variation in nutrient availability may or may not be an important consideration. The evolutionary forces that have shaped the breeding success of males usually are fundamentally different from those acting on females and, by implication, the environmental controls governing reproduction probably also often differ either qualitatively or quantitatively in the two sexes. Mammals often live in habitats where energetic and nutrient challenges vary seasonally, even in the tropics. When seasonal breeding is required, a mammal may use a predictor such as photoperiod or a secondary plant compound to prepare metabolically for reproduction. A reasonable argument can be made, however, that opportunistic breeding, unenforced by a predictor, may be the most prevalent strategy extant among today's mammals. Social cues can have potent modulating actions. They can act either via discrete neural and endocrine pathways to alter specific processes such as ovulation, or they can induce nonspecific emotional states that secondarily affect reproduction. Many major gaps remain in our knowledge about the environmental regulation of mammalian reproduction. For one, we have a paucity of information about the annual patterns of breeding and about the mechanisms controlling these patterns in the most common mammals on the planet-the small to average-sized mammals living in the tropics. We probably have only a shallow conceptualization of the way available energy and nutrients control reproduction and, likewise, we may have only a narrow view of the potential kinds and uses of seasonal predictors. Finally, we have little appreciation of the way environmental cues interact with each other to control reproduction.     

Density dependence slows invader spread in fragmented landscapes

Patchiness is a defining characteristic of most natural and anthropogenic habitats, yet much of our understanding of how invasions spread has come from models of spatially homogeneous environments. Except for populations with Allee effects, an invader's growth rate when rare and dispersal determine its spread velocity; intraspecific competition has little to no influence. How this result might change with landscape patchiness, however, is poorly understood. We used simulation models and their analytical approximations to explore the effect of density dependence on the spread of annual plant invaders moving through heterogeneous landscapes with gaps in suitable habitat. We found that landscape patchiness and discrete invader population size interacted to generate a strong role for density dependence. Intraspecific competition greatly slowed the spread of invasions through patchy landscapes by regulating how rapidly a population could produce enough seeds to surpass habitat gaps. Populations with continuously varying density showed no such effect of density dependence. We adapted a stochastic dispersal model to approximate spread when gap sizes were small relative to the mean dispersal distance and a Markov chain approximation for landscapes with large gaps. Our work suggests that ecologists must consider reproduction at both low and high densities when predicting invader spread.     

Density dependence in a recovering osprey population: demographic and behavioural processes

1. Understanding how density-dependent and independent processes influence demographic parameters, and hence regulate population size, is fundamental within population ecology. We investigated density dependence in growth rate and fecundity in a recovering population of a semicolonial raptor, the osprey Pandion haliaetus [Linnaeus, 1758], using 31 years of count and demographic data in Corsica. 2. The study population increased from three pairs in 1974 to an average of 22 pairs in the late 1990s, with two distinct phases during the recovery (increase followed by stability) and contrasted trends in breeding parameters in each phase. 3. We show density dependence in population growth rate in the second phase, indicating that the stabilized population was regulated. We also show density dependence in productivity (fledging success between years and hatching success within years). 4. Using long-term data on behavioural interactions at nest sites, and on diet and fish provisioning rate, we evaluated two possible mechanisms of density dependence in productivity, food depletion and behavioural interference. 5. As density increased, both provisioning rate and the size of prey increased, contrary to predictions of a food-depletion mechanism. In the time series, a reduction in fledging success coincided with an increase in the number of non-breeders. Hatching success decreased with increasing local density and frequency of interactions with conspecifics, suggesting that behavioural interference was influencing hatching success. 6. Our study shows that, taking into account the role of non-breeders, in particular in species or populations where there are many floaters and where competition for nest sites is intense, can improve our understanding of density-dependent processes and help conservation actions.     

Density dependence and environmental factors affect population stability of an agricultural pest and its specialist parasitoid

Host–parasitoid dynamics are intrinsically unstable unless the risk of parasitism is sufficiently heterogeneous among hosts. Spatial aggregation of parasitoids can contribute to this heterogeneity, stabilising host–parasitoid population dynamics and thereby reducing pest outbreaks. We examined the spatial distribution of mango gall fly (Procontarinia matteiana, Kiefer and Cecconi), a non-native pest of South African mango orchards, which is controlled by a single parasitoid (Chrysonotomyia pulcherrima, Kerrich). We assessed whether spatial aggregation of parasitoids is associated with proximity to natural vegetation and/or to host density-dependent and host density-independent factors at three spatial scales. We found evidence for higher parasitism rates near natural vegetation at the field scale, and inverse host-density dependent and density-independent parasitoid aggregation at both the leaf scale and field scale. Therefore, we conclude that natural vegetation plays a role in promoting stabilising aggregation of parasitoids, possibly through provision of non-host resources (nectar, pollen), in this system.