Natural selection as an emergent process: instructional implications

Student reasoning about cases of natural selection is often plagued by errors that stem from miscategorising selection as a direct, causal process, misunderstanding the role of randomness, and from the intuitive ideas of intentionality, teleology and essentialism. The common thread throughout many of these reasoning errors is a failure to apply ‘population thinking’. Students fail to recognise that natural selection refers to changes in the distribution of certain traits at the population level, the collective, resulting from interactions between individual organisms and their environment at the next lower level in the system. Processes like selection are emergent processes in hierarchical systems, where patterns in a collective are generated by interactions at the lower level. By helping students develop an emergent process schema that enables them to recognise that even random interactions at one level in a system can generate predictable patterns at a higher level, their understanding of natural selection should improve. Some studies have shown this to be an effective approach for teaching other emergent processes. Instructional recommendations based on these studies are presented here, but more research is needed to determine the full extent to which this approach can improve students’ understanding.     

Resources Alter the Structure and Increase Stochasticity in Bromeliad Microfauna Communities

Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down interactions (predators) and dispersal at two spatial scales in the field. We found that resource addition strongly increased the abundance and reduced the richness of microfauna communities. Community composition shifted in a predictable way towards assemblages dominated by flagellates and ciliates but with lower abundance and richness of algae and amoebae. While all functional groups responded strongly and predictably to resource addition, similarity among communities at the species level decreased, suggesting a role of stochasticity in species-level assembly processes. Dispersal limitation did not affect the communities. Since our design excluded potential priority effects we can attribute the differences in community similarity to increased demographic stochasticity of resource-enriched communities related to erratic changes in population sizes of some species. In contrast to resources, predators and environmental conditions had negligible effects on community structure. Our results demonstrate that bromeliad microfauna communities are strongly controlled by bottom-up forces. They further suggest that the relative importance of stochasticity may change with productivity and with the organizational level at which communities are examined.     

Disentangling spatio‐temporal processes in a hierarchical system: a case study in fisheries discards

In the last decade, various spatial and temporal methodologies were developed to investigate the processes that drive ecological and evolutionary patterns. However, these methods frequently fail to acknowledge that the observed patterns result from the overlap of different underlying processes. In order to understand how the patterns are formed, we must have recourse to methods that allow us to disentangle these simultaneous processes. Here we develop a hierarchical spatial predictive process (PP) combined with a separable temporal PP to disentangle and describe those overlapping processes in one very frequent setting in ecology and evolution: multilevel spatio‐temporally indexed data. We present our methodology through a case study of fisheries discards and investigate for example whether the inclusion of the hierarchical structure and the temporal processes of the system alter the observed spatial patterns. Recently it is recognized that understanding the processes driving discards is essential to sustainably manage and conserve marine resources. The results show that consideration of multiple underlying processes dramatically changes the pattern and characteristics of the discards hot‐ and coldspots. In the Irish Sea, the inclusion of the hierarchical structure of the system leads to the reduction of the hot‐ and coldspots. Simultaneously, our model identifies key bi‐annual fluctuations in the temporal process which, together with the variance associated at the level of individual fishing trips in the hierarchical structure of the data explained most of the variance driving discards. Whether the hierarchical, spatial and temporal processes are considered together or not can profoundly alter our understanding of what constitutes an appropriate mitigation measure. Misidentification of hotspots can culminate in inappropriate mitigation practices which can sometimes be irreversible. As the proposed method offers a unified approach for understanding the processes that drive observed patterns, many areas in ecology such as conservation and epidemiological studies can benefit from its use, increasing the effectiveness of management plans.     

Intraspecific facilitation: a missing process along increasing stress gradients – insights from simulated shrub populations

In recent years many field studies have been conducted to assess the relative importance of facilitation and competition in structuring vegetation communities in different environments. Herein, we present a simulation model which systematically explores the relative importance of intra‐specific facilitation and competition between adult shrubs and seedlings for spatial pattern formation. A grid‐based simulation model was constructed and calibrated using data collected in the field from Sarcopoterium spinosum populations in Israel to simulate population dynamics along a rainfall gradient. A series of simulation experiments was conducted in which manipulations of seedling survival probabilities were carried out to assess the relative importance of these processes in generating spatial patterns. Increased survival probabilities of first‐year shrubs in open areas were used to simulate competition effects, while increased survival probabilities in the vicinity of shrubs were used to simulate facilitation effects. Simulation results were then compared to shrub spatial patterns observed in the field. The results indicate that facilitation is not an important process in generating intra‐specific spatial patterns. Rather, in mesic environments with high precipitation, competition is the dominant process generating spatial patterns, resulting in regular spacing of shrubs, similarly to the patterns observed in the field (L(h) values<0). In arid sites, where precipitation values are lower, and stress conditions are higher, the dominant process generating spatial patterns was random mortality due to drought conditions. The resulting spatial patterns in this case are random (L(h)～0), whereas observed field populations exhibited clumped patterns (L(h)>0). We conclude that as stress conditions increase, the importance of intraspecific neighborhood interactions decrease whereas the importance of environmental factors increase in dictating intra‐specific spatial pattern formation. Consequently in mesic environments intra‐specific competition among adults determines the emerging patterns, while intraspecific facilitation is a negligible process.     

Biophysical mechanisms for morphogenetic progressions at the shoot apex.

Leaf primordia, first visible as small bumps, are produced in a cyclical pattern at the edges of the shoot apex, a smooth region at the top of the stem. Their formation is a biomechanical process. This review first considers hypothetical construction mechanisms and then summarizes research that provides information about how and where the primordia are made. Studies of growth at the primordium site indicate the importance of growth parallel to the surface in generating the forces for primordium emergence. The symmetry of the pattern of reinforcement by cellulose microfibrils correlates with the subsequent pattern of primordium production. Finite element models of the apex reveal that lateral bulging of the apex results in a gradient of shear stress, with high shear at the future primordium site. In contrast, tension parallel to the surface is lowest at the primordium site. Response of apical surface tissue to punctures indicates that an existing primordium can exert a pulling force tangential to its base and a compressive force perpendicular to its base. These observations lead to identification of a continuous biophysical cycle for apex morphogenesis, in which most of the steps are direct physical consequences of the previous step. Biophysical processes, subject to input from genetic, hormonal, and environmental sources, are thus involved in the construction and patterning of leaf primordia.     

The relationship between body size and population abundance in animals

On average, large-bodied species live at lower densities than small-bodied ones. Early studies suggested that population densities might scale so that the energy use of a population is independent of body size. However, recent work shows that, at the scale of local communities, this is rarely true and that the pattern varies among taxonomic or ecological subsets of those communities. Energetic considerations may only be relevant to the densities of more abundant species. In fact, within natural assemblages o f organisms, the underlying relationship is very variable; in subsets of those assemblages, ecological processes such as competition may structure abundance patterns.     

Bifurcations of emergent bursting in a neuronal network

Complex neuronal networks are an important tool to help explain paradoxical phenomena observed in biological recordings. Here we present a general approach to mathematically tackle a complex neuronal network so that we can fully understand the underlying mechanisms. Using a previously developed network model of the milk-ejection reflex in oxytocin cells, we show how we can reduce a complex model with many variables and complex network topologies to a tractable model with two variables, while retaining all key qualitative features of the original model. The approach enables us to uncover how emergent synchronous bursting can arise from a neuronal network which embodies known biological features. Surprisingly, the bursting mechanisms are similar to those found in other systems reported in the literature, and illustrate a generic way to exhibit emergent and multiple time scale oscillations at the membrane potential level and the firing rate level.     

Distribution patterns of vascular plants in lakes – the role of metapopulation dynamics

We investigated the relative importance of metapopulation processes versus environmental conditions for the distribution of freshwater plants in 51 adjacent lakes in southern Sweden. Each lake was surveyed by snorkeling in a zigzag pattern over the littoral zone, and all aquatic vascular plants as well as water colour, Sphagnum -dominated shore, bottom substrate, littoral zone width and Secchi-depth were recorded. Data on lake area and altitude was taken from topographical maps. Multiple generalized linear regressions were used to test the significance of factors influencing species number and incidence of specific species in lakes. The best combination of predictor variables for species number was lake area (β=0.52), area of upstream lakes (β=0.23), and height above sea-level (β=−0.21) (whole model R²=0.52). The presence-absence patterns of most of the studied species were affected positively by connectivity, measured both as geographical proximity of the lakes and as connection to upstream lakes. The level of effect of connectivity on species incidence was also correlated with life history traits. The distributions of emergent species were less affected by connectivity than those of submerged and floating-leafed types, reflecting that emergent plants can occur in habitat patches surrounding the lakes. The results indicate that metapopulation processes affect the distribution of freshwater plants, but that their relative importance vary widely among species.     

The importance of integration and scale in the arbuscular mycorrhizal symbiosis

The arbuscular mycorrhizal (AM) fungus contributes to system processes and functions at various hierarchical organizational levels, through their establishment of linkages and feedbacks between whole-plants and nutrient cycles. Even though these fungal mediated feedbacks and linkages involve lower-organizational level processes (e.g. photo-assimilate partitioning, interfacial assimilate uptake and transport mechanisms, intraradical versus extraradical fungal growth), they influence higher-organizational scales that affect community and ecosystem behavior (e.g. whole-plant photosynthesis, biodiversity, nutrient and carbon cycling, soil structure). Hence, incorporating AM fungi into research directed at understanding many of the diverse environmental issues confronting society will require knowledge of how these fungi respond to or initiate changes in vegetation dynamics, soil fertility or both. Within the last few years, the rapid advancement in the development of analytical tools has increased the resolution by which we are able to quantify the mycorrhizal symbiosis. It is important that these tools are applied within a conceptual framework that is temporally and spatially relevant to fungus and host. Unfortunately, many of the studies being conducted on the mycorrhizal symbiosis at lower organizational scales are concerned with questions directed solely at understanding fungus or host without awareness of what the plant physiologist or ecologist needs for integrating the mycorrhizal association into larger organizational scales or process levels. We show by using the flow of C from plant-to-fungus-to-soil, that through thoughtful integration, we have the ability to bridge different organizational scales. Thus, an essential need of mycorrhizal research is not only to better integrate the various disciplines of mycorrhizal research, but also to identify those relevant links and scales needing further investigation for understanding the larger-organizational level responses. The U.S. Government's right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged. This revised version was published online in June 2006 with corrections to the Cover Date.     

Pattern formation during vasculogenesis

Vasculogenesis, the assembly of the first vascular network, is an intriguing developmental process that yields the first functional organ system of the embryo. In addition to being a fundamental part of embryonic development, vasculogenic processes also have medical importance. To explain the organizational principles behind vascular patterning, we must understand how morphogenesis of tissue level structures can be controlled through cell behavior patterns that, in turn, are determined by biochemical signal transduction processes. Mathematical analyses and computer simulations can help conceptualize how to bridge organizational levels and thus help in evaluating hypotheses regarding the formation of vascular networks. Here, we discuss the ideas that have been proposed to explain the formation of the first vascular pattern: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and sprouting guided by cell–cell contacts. Birth Defects Research (Part C) 96:153–162, 2012. © 2012 Wiley Periodicals, Inc.     

Scaling analysis of coral reef systems: an approach to problems of scale

Dimensional analysis and scaling are related, semi-formal procedures for capturing the essential process(es) controlling the behaviour of a complex system, and for describing the functional relationships between them. The techniques involve the parameterization of natural processes, the identification of the temporal and spatial scales of variation of processes, and the evaluation of potential interactions between processes referenced to those scales using non-dimensional (scaled) parameters. Scaling approaches are increasingly being applied to a broad range of marine ecological problems, with the aims of assessing the relative importance of physical and biological parameters in controlling variation in process rates, and placing limits on the ability of one process to affect another. The value of the approach to coral reef research lies in the conceptualization of relationships between discipline-specific processes, and the evaluation of scale-dependent processes across the large range of spatial and temporal scales which pertain to coral reefs. Characteristic scales of physical, geological and biological processes exhibit different patterns of distribution along the temporal dimension. Scaling arguments based on examples from reef systems indicate that a large group of biological and biogeochemical processes are strongly influenced by hydrodynamic processe occuring at similar time scales within the range from about on hour to one year. We argue that scaling approaches to process-related problems are pre-requisite to interdisciplinary research on coral reefs.     

Determinism and probability in the development of the cell theory

A return to Claude Bernard's original use of the concept of 'determinism' displays the fact that natural laws were presumed to rule over all natural processes. In a more restricted sense, the term boiled down to a mere presupposition of constant determinant causes for those processes, leaving aside any particular ontological principle, even stochastic. The history of the cell theory until around 1900 was dominated by a twofold conception of determinant causes. Along a reductionist trend, cells' structures and processes were supposed to be accounted for through their analysis into detailed partial mechanisms. But a more holistic approach tended to subsume those analytic means and the mechanism involved under a program of global functional determinations. When mitotic and meiotic sequences in nuclear replication were being unveiled and that neo-Mendelian genetics was being grafted onto cytology and embryology, a conception of strict determinism at the nuclear level, principally represented by Wilhelm Roux and August Weismann, would seem to rule unilaterally over the mosaic interpretation of the cleavage of blastomeres. But, as shown by E.B. Wilson, in developmental processes there occur contingent outcomes of cell division which observations and experiments reveal. This induces the need to admit 'epigenetic' determinants and relativize the presumed 'preformation' of thedevelopmental phases by making room for an emergent order which the accidental circumstances of gene replication would trigger?on.     

The spatial structure of populations

1. Studies of the spatio-temporal dynamics and structure of populations have identified many categories of population type. However, recognized categories intergrade, making it difficult to assign empirical population systems to single categories.
2. We suggest that most population categories can be arranged along two axes that combine per capita birth (B), death (D), emigration (E) and immigration (I) rates. The 'Compensation Axis' describes the source-sink component of population structure, with source populations exporting individuals (B > D, E > I) and sinks and pseudosinks consuming individuals (B < D, E < I). The 'Mobility Axis' describes the involvement of a local population in regional (I + E) rather than local (B + D) processes, running from separate populations, through metapopulations, to patchy populations.
3. Each sample area within a spatially structured population system can potentially be assigned to a position along each of these axes, with individual sample areas weighted by local population size. The positions of these sample areas and their relative weightings allow the relative importance of different types of process to be judged. A worked exampled is provided, using the butterfly Hesperia comma . This approach shifts the emphasis from pattern (categories that real population systems do not fit) onto process.
4. In many systems, continuous variation in habitat quality and demographic parameters make clear distinctions between 'habitat' and 'non-habitat' difficult to sustain. In such cases, we advocate the use of a spatial grid system, with effects of patch size and isolation combined into a single, weighted distance function (neighbourhood).
5. The relative importance of different processes depends on the spatial scale at which the system is observed. This again emphasizes the value of a process-based approach.     

Relative phase dynamics in perturbed interlimb coordination: the effects of frequency and amplitude

Sch?ner [Sch?ner G (1995) Ecol Psychol 7: 291-314] argued that the relative phase dynamics of rhythmic interlimb coordination may be attributed to the timing level in that the stability properties of the relative phase are largely independent of dynamical principles operating at the goal level, such as those related to the maintenance of a particular amplitude or target position. Yet, according to the coupling functions in the coupled oscillator model proposed by Haken et al. [Haken H, Kelso JAS, Bunz H (1985) Biol Cybern 51: 347-356], the effect of frequency on the stability properties of relative phase is either wholly or partially mediated by frequency-induced changes in amplitude, implying that the relative phase dynamics strongly depends on spatial factors. In order to distinguish between these contrasting interpretations of the organizational principles underwriting the phase dynamics of interlimb coordination, an experiment was conducted in which the effects of frequency and amplitude on the stability of relative phase were separated. Six subjects performed both in-phase and antiphase coordination patterns at seven different frequencies and three different amplitudes. Two measures of pattern stability were used, the standard deviation of relative phase and the exponent of the relaxation process following phasic perturbations of relative phase. According to both measures, pattern stability decreased with increasing frequency, whereas the amplitude manipulation only had a significant effect on the standard deviation of relative phase. This result was interpreted to imply that the organizational principles at the (relative) timing level are affected only moderately by task constraints pertaining to the goal level, and that models of interlimb coordination in which amplitude coupling plays a partial or subordinate role should be preferred above models relying solely on amplitude coupling.     

Did natural selection or genetic drift produce the cranial diversification of neotropical monkeys?

A central controversy among biologists is the relative importance of natural selection and genetic drift as creative forces shaping biological diversification (Fisher 1930; Wright 1931). Historically, this controversy has been an effective engine powering several evolutionary research programs during the last century (Provine 1989). While all biologists agree that both processes operate in nature to produce evolutionary change, there is a diversity of opinion about which process dominates at any particular organizational level (from DNA and proteins to complex morphologies). To address this last level, we did a broadscale analysis of cranial diversification among all living New World monkeys. Quantitative genetic models yield specific predictions about the relationship between variation patterns within and between populations that may be used to test the hypothesis that genetic drift is a sufficient explanation for morphological diversification. Diversity at several levels in a hierarchy of taxonomic/phylogenetics relationship was examined from species within genera to families within superfamilies. The major conclusion is that genetic drift can be ruled out as the primary source of evolutionary diversification in cranial morphology among taxa at the level of the genus and above as well as for diversification of most genera. However, drift may account for diversification among species within some Neotropical primate genera, implying that morphological diversification associated with speciation need not be adaptive in some radiations.     

Topographic distributions of emergent trees in tropical forests of the Osa Peninsula,Costa Rica

Tropical rainforests are reservoirs of terrestrial carbon and biodiversity. Large and often emergent trees store disproportionately large amounts of aboveground carbon and greatly influence the structure and functioning of tropical rainforests. Despite their importance, controls on the abundance and distribution of emergent trees are largely unknown across tropical landscapes. Conventional field approaches are limited in their ability to characterize patterns in emergent trees across vast landscapes with varying environmental conditions and floristic composition. Here, we used a high‐resolution light detection and ranging (LiDAR) sensor aboard the Carnegie Airborne Observatory Airborne Taxonomic Mapping System (CAO‐AToMS) to examine the abundance and distribution of tall emergent tree crowns (ETC) relative to surrounding tree crowns (STC) across the Osa Peninsula, a geologically and topographically diverse region of Costa Rica. The abundance of ETC was clearly influenced by fine‐scale topographic variation, with distribution patterns that held across a variety of geologic substrates. Specifically, the density of ETC was much greater on lower slopes and in valleys, compared to upper slopes and ridges. Furthermore, using the CAO high‐fidelity imaging spectrometer, ETC had a different spectral signature than that of STC. Most notably, ETC had lower remotely sensed foliar nitrogen than STC, which was verified with an independent field survey of canopy leaf chemistry. The underlying mechanisms to explain the topographic‐dependence of ETCs and linkages to canopy N are unknown, and remain an important area of research.     

Range size heritability in Carnivora is driven by geographic constraints

Range size heritability refers to an intriguing pattern where closely related species occupy geographic ranges of similar extent. Its existence may indicate selection on traits emergent only at the species level, with interesting consequences for evolutionary processes. We explore whether range size heritability may be attributable to the fact that range size is largely driven by the size of geographic domains (i.e., continents, biomes, areas given by species' climatic tolerance) that tend to be similar in phylogenetically related species. Using a well-resolved phylogeny of Carnivora, we show that range sizes are indeed constrained by geographic domains and that the phylogenetic signal in range sizes diminishes if the domain sizes are accounted for. Moreover, more detailed delimitation of species' geographic domain leads to a weaker signal in range size heritability, indicating the importance of definition of the null model against which the pattern is tested. Our findings do not reject the hypothesis of range size heritability but rather unravel its underlying mechanisms. Additional analyses imply that evolutionary conservatism in niche breadth delimits the species' geographic domain, which in turn shapes the species' range size. Range size heritability patterns thus emerge as a consequence of this interplay between evolutionary and geographic constraints.