Spatial Ecological Hierarchies: Coexistence on Heterogeneous Landscapes via Scale Niche Diversification

Spatially heterogeneous environments are generally characterized by nested landscape patterns with resource aggregations on several scales. Empirical studies indicate that such nested landscape patterns impose selection constraints on the perceptive scales of animals, but the underlying selection mechanisms are unclear. We investigated the selection dynamics of perceptive scale within a spatial resource utilization model, where the environment is characterized by its resource distribution and species differ in their perceptive scales and resource preemption capabilities. Using three model landscapes with various resource distributions, we found that the optimal perceptive scale is determined by scale-specific attributes of the landscape pattern and that the number of coexisting species increases with the number of characteristic scales. Based on the results of this model, we argue that resource aggregations on different scales act as distinct resources and that animal species of particular perceptive scales are superior in utilizing resource aggregations of comparable spatial extent. Due to the allometric relationship between body size and perceptive scale, such fitness difference might result in discontinuous body mass distributions.     

Dynamic Landscapes, Stability and Ecological Modeling

The image of a ball rolling along a series of hills and valleys is an effective heuristic by which to communicate stability concepts in ecology. However, the dynamics of this landscape model have little to do with ecological systems. Other landscape representations, however, are possible. These include the particle on an energy landscape, the potential landscape, and the Lyapunov function landscape. I discuss the dynamics that these representations admit, and the application of each to ecological modeling and the analysis and representation of stability. CWP is a Postdoctoral Fellow with the Oak Ridge Institute for Science and Education     

Dynamic Mutual Adaptation: Human-Animal Interaction in Reindeer Herding Pastoralism

Most of the existing anthropological literature that recognizes human-animal interaction as being at the core of nomadic pastoralism focuses on nomads as the only active agents of this interaction. Nomads interact with their animals by either adapting their actions to animal behavior or by changing this behavior in ways to suit them. Based on empirical material from two groups of reindeer herding nomads in northern Russia, we suggest that human-animal interaction in nomadic pastoralism can be better understood as being the result of a dynamic mutual behavioral adaptation. In the process of this adaptation, animals change their behavior in response to the herders’ actions, which in turn leads to a responsive change to herders’ patterns of actions, etc. We argue that this approach can account for the differences in both animal behavior and herding technologies across nomadic pastoralist cultures, as well as for some of the divergent developments within these cultures.     

Investigating Morphospace Occupation in Multi-Scale Ecological and Evolutionary Data Using Regression Tree: Case Studies and Perspectives

A key challenge in ecology and evolutionary biology is to explain the origin, structure and temporal patterns of phenotypic diversity. With regard to the potentially complex determinism of phenotypic differences, the issue should be comprehended in a general view, across multiple scales and an increasing number of phenomic studies investigate shape variation through large taxonomic, biogeographic or temporal scales. In this context, there is an ever-increasing need to develop new tools for a coherent understanding of morphospace occupation by disentangling and quantifying the main determinants of phenotypic changes. The present study briefly introduce the possibility to use multivariate regression tree technique to cope with morphological data, as embedded in a geometric morphometric framework. It emphasizes that hierarchical partitioning methods produce a hierarchy between causal variables that may help analyzing complexity in multi-scale ecological and evolutionary data. I therefore suggest that morphological studies would benefit from the combined use of the classical statistical models with rapidly emerging and diversifying methods of machine-learning. Doing so allows one to primary explore in an extensive exploratory manner the hierarchy of nested organisational levels underlying morphological variation, and then conduct hypothesis-driven analysis by focusing on a relevant scale or by investigating the appropriate model that reflects hypothesized nested influence of explanatory variables. The outlined approach may help investigating morphospace occupation in an explicitly hierarchical quantitative context.     

Investigating the Ecological and Evolutionary Significance of Plant Growth Form using Stochastic Simulation

Results from a computer program which simulates the growth ofplants by stochastic simulation are presented. The simulatedplants grow in an acceptably realistic fashion, and can be grownwith any combination of main and lateral branch angle branchprobability and internode distance Growth rates are shown todepend upon branch probability, and whilst the growth of monopodialsystems is shown to be relatively independent of the angle ofbranching, that of sympodial systems is shown to be dependentupon branch angle. Sympodial systems outcompete monopodial systemsunder some simulated conditions. The relationship between internodedistance and the size of environmental patches is shown to becrucial for successful growth. Computer simulation, stochastic model, growth form, branching     

An Evolutionary Analysis of Antigen Processing and Presentation across Different Timescales Reveals Pervasive Selection

The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage.We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses.     

Plant-soil Interactions: Ecological Aspects and Evolutionary Implications

Building on the concept of plants as ecosystem engineers, and on published information on effects of particular plant species on soils, we review the evidence that such effects can provide a positive feedback to such plants. Based on case studies involving dune formation by Marram grass, N supply by N2-fixing plants, depression of N availability by ericaceous plants, islands of fertility in deserts, mull- and mor-forming temperate forest trees, and formation of peatbogs, as well as similar other cases, we conclude that there is strong evidence for plant-soil feedbacks in a variety of ecosystems. We argue, moreover, that these feedbacks could have played a role in the evolution of the plant species in question. These ideas are based mainly on correlative observations, and need further testing.     

Animals in Schools: Processes and Strategies in Human-Animal Education

Abstract

In this study we tested the hypothesis that the process of training a non-human primate (NHP) affects it's general behavior patterns, outside of training. A group of Abyssinian colobus monkeys (Colobus guereza, n = 8), housed at Paignton Zoo, UK, were observed for four 12-day periods. Behaviors were noted prior to training, using positive reinforcement to achieve oral examinations, and each month for three months after training had started. These data were used to construct daily activity budgets and investigate social behaviors (both colobus–colobus and colobus–human). A comparison of these data (using doubly repeated measures MANOVAs) showed activity budget (F_(3,3) = 9.8, λ = 0.4, p < 0.001) and colobus-initiated interactions with people (F_(3,2) = 16.6, λ = 0.3, p < 0.001) differed significantly across the four observation periods. Resting behavior was negatively correlated with feeding behavior (Pearson: n = 56, r = -0.25, p < 0.05); this relationship was considered to be independent of the onset of training. The significant decline in colobus-initiated interactions with the public appeared to be a direct result of the training.

The results in this study showed that the implementation of training reduced colobus–human interactions. Two reasons are suggested in this paper to account for these unexpected results; either or both of these explanations may be true. The increased level of keeper–colobus interactions necessary for training may have acted to socialize the colobus to humans, so that they habituated to the general presence of humans. Equally, the training sessions may have provided the colobus with predictable interactions with humans that provided rewards, outside of which colobus-initiated interactions were not worthwhile.

Training in this situation was found to be beneficial for the colobus and did not adversely affect the behavior of the colobus outside of the training sessions. It is concluded that caution should be taken when instigating training as part of captive primate management, due to species differences and the paucity of studies that have quantified the impact of training on zoo primate biology. What is greatly needed is more studies which are able to empirically compare the biology (behavior and physiology) of zoo housed primates before and after training has been implemented.     

Persistence of Dispersal-limited Species in Structured Dynamic Landscapes

Dynamic landscape models have generally assumed random distributions of habitat although real landscapes show spatial organization at many scales. To explore the role of spatial structure in determining the frequency of dispersal-limited forest species, we used a cellular landscape model divided into two zones. Zones were distributed in a random, clustered, or regular spatial pattern. Within each zone habitat cells were randomly destroyed and regenerated, and habitat density and turnover rate were systematically varied. A hypothetical habitat-limited species dispersed between adjacent habitat cells. All trials showed a reduced species frequency relative to a static landscape. Reduction was greater at low habitat density (P = 0.30) than at high density (0.90) suggesting the importance of habitat connectivity in controlling species frequency. The greatest reduction occurred when habitat was concentrated in a small, regularly distributed zone at low habitat density reflecting the enforced isolation of individual habitat cells. Very little reduction was observed when habitat cells were packed into a small clustered zone, a situation promoting connectivity between cells. Moderate–severe frequency reduction occurred when habitat turnover was concentrated in a clustered zone at high habitat density, but little was observed when turnover was widely distributed in a regular or random pattern. These results can be interpreted in terms of a source-sink function in which spatial pattern controlled the degree of contact between landscape zones and determined opportunities for dispersal between habitat cells. We conclude that clustering of forest habitat has the potential to maintain herb species frequency in sparsely forested landscapes. Conversely, clustering of forest disturbance in heavily forested regions, or regular distribution of forest stands (as often occurs in agricultural regions) creates areas which are difficult to colonize, and should be avoided.     

Using Ecological Niche Models and Niche Analyses to Understand Speciation Patterns: The Case of Sister Neotropical Orchid Bees

The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species.     

Ecological Niche Conservatism in Doucs (Genus Pygathrix)

The impressive diversity and unique distribution of primate taxa in Southeast Asia creates a region of interesting biogeography and evolutionary history that remains poorly understood. The three species in the Asian colobine genus Pygathrix (P. cinerea, P. nemaeus, and P. nigripes) appear to follow the unique distribution pattern, replacing one another along the north–south axis. However, the evolutionary history and taxonomic status within Pygathrix is currently debated. We constructed climate-based ecological niche models (ENMs) for the three species, using six environmental variables, to confirm that the bioclimate envelopes of Pygathrix cinerea, P. nemaeus, and P. nigripes follow the north–south gradient. We also used the ENMs to test whether the three species lack ecological exchangeability, meaning differentiation among factors that define the fundamental niche, and whether they exhibit ecological niche conservatism, or the tendency for related species to differ less ecologically than might be expected by the climate available to each species. Our ENMs for Pygathrix followed a north–south gradient as expected, with P. nemaeus extending from ca. 14°N to 21°N, P. cinerea from 14°N to 16°N, and P. nigripes from 11°N to 13.5°N. This study presents the first use of ENMs for doucs that yield significant predictive ability based only on climatic variables. The models are significantly different for all three species, supporting a lack of ecological exchangeability between them, as well as the recent elevation of Pygathrix cinerea to species status. Importantly, Pygathrix cinerea and P. nemaeus show evidence of ecological niche conservatism, which lends support to the occurrence of an allopatric speciation event. This result also suggests that the current overlapping distribution of Pygathrix cinerea and P. nemaeus is the result of secondary contact. The north–south distribution gradient, which exists in similar form among other groups of sister taxa in the region, may be attributed to a zoogeographic barrier, vicariance, or current or historical climatic shifts.