Flavia Maria Darcie Marquitti

Biodiversity, Species Interactions and Ecological Networks in a Fragmented World

Biodiversity is organised into complex ecological networks of interacting species in local ecosystems, but our knowledge about the effects of habitat fragmentation on such systems remains limited. We consider the effects of this key driver of both local and global change on both mutualistic and antagonistic systems at different levels of biological organisation and spatiotemporal scales. There is a complex interplay of patterns and processes related to the variation and influence of spatial, temporal and biotic drivers in ecological networks. Species traits (e.g. body size, dispersal ability) play an important role in determining how networks respond to fragment size and isolation, edge shape and permeability, and the quality of the surrounding landscape matrix. Furthermore, the perception of spatial scale (e.g. environmental grain) and temporal effects (time lags, extinction debts) can differ markedly among species, network modules and trophic levels, highlighting the need to develop a more integrated perspective that considers not just nodes, but the structural role and strength of species interactions (e.g. as hubs, spatial couplers and determinants of connectance, nestedness and modularity) in response to habitat fragmentation. Many challenges remain for improving our understanding: the likely importance of specialisation, functional redundancy and trait matching has been largely overlooked. The potentially critical effects of apex consumers, abundant species and super-generalists on network changes and evolutionary dynamics also need to be addressed in future research. Ultimately, spatial and ecological networks need to be combined to explore the effects of dispersal, colonisation, extinction and habitat fragmentation on network structure and coevolutionary dynamics. Finally, we need to embed network approaches more explicitly within applied ecology in general, because they offer great potential for improving on the current species-based or habitat-centric approaches to our management and conservation of biodiversity in the face of environmental change.

Analysis of a hyper‐diverse seed dispersal network: modularity and underlying mechanisms

Mutualistic interactions involving pollination and ant-plant mutualistic networks typically feature tightly linked species grouped in modules. However, such modularity is infrequent in seed dispersal networks, presumably because research on those networks predominantly includes a single taxonomic animal group (e.g. birds). Herein, for the first time, we examine the pattern of interaction in a network that includes multiple taxonomic groups of seed dispersers, and the mechanisms underlying modularity. We found that the network was nested and modular, with five distinguishable modules. Our examination of the mechanisms underlying such modularity showed that plant and animal trait values were associated with specific modules but phylogenetic effect was limited. Thus, the pattern of interaction in this network is only partially explained by shared evolutionary history. We conclude that the observed modularity emerged by a combination of phylogenetic history and trait convergence of phylogenetically unrelated species, shaped by interactions with particular types of dispersal agents.

The structure of ant–plant ecological networks: Is abundance enough?

Knowledge of the mechanisms that shape biodiversity is essential to understand the ecological and evolutionary dynamics of interacting species. Recent studies posit that most of the organization of mutualistic networks is shaped by differences in species abundance among interacting species. In this study, we examined the mutualism involving plants with extrafloral nectaries and their associated ants. We show empirically that the difference in abundance among ants on vegetation partially explains the network structure of mutualistic interactions and that it is independent of ant species compositions: an ant species that is abundant usually interacts with more plant species. Moreover, nested networks are generated by simple variation in ant abundance on foliage. However, in ant-plant mutualistic networks, nestedness was higher than in networks describing the occurrence of ants on plants without a food resource. Additionally, the plant and ant species with the highest number of interactions within these networks interacted more among themselves than expected under the assumption of an abundance-based, random mixing of individuals. We hypothesize that the dominance of these ant species occurs because these ants are able to outcompete other ant species when feeding on extrafloral nectaries and because of the presence of ecophysiological adaptations to utilize liquid food.

Modelling the heart as a communication system

Electrical communication between cardiomyocytes can be perturbed during arrhythmia, but these perturbations are not captured by conventional electrocardiographic metrics. We developed a theoretical framework to quantify electrical communication using information theory metrics in two-dimensional cell lattice models of cardiac excitation propagation. The time series generated by each cell was coarse-grained to 1 when excited or 0 when resting. The Shannon entropy for each cell was calculated from the time series during four clinically important heart rhythms: normal heartbeat, anatomical reentry, spiral reentry and multiple reentry. We also used mutual information to perform spatial profiling of communication during these cardiac arrhythmias. We found that information sharing between cells was spatially heterogeneous. In addition, cardiac arrhythmia significantly impacted information sharing within the heart. Entropy localized the path of the drifting core of spiral reentry, which could be an optimal target of therapeutic ablation. We conclude that information theory metrics can quantitatively assess electrical communication among cardiomyocytes. The traditional concept of the heart as a functional syncytium sharing electrical information cannot predict altered entropy and information sharing during complex arrhythmia. Information theory metrics may find clinical application in the identification of rhythm-specific treatments which are currently unmet by traditional electrocardiographic techniques.

Nestedness across biological scales

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks.

Registering the evolutionary history in individual-based models of speciation

Phylogenetic trees are systematic tools to describe relatedness among species. The inference of biological trees aims to find the best phylogenetic tree that reconstructs the evolution of a group of species. Computer models that simulate the speciation process can track population dynamics and record information about genealogic relationships. In this paper we describe a procedure for the construction of phylogenetic trees in individual based models of evolution and speciation. Keeping track of the parental relationships of all members of the population we set up a matrix containing the times to the most recent common ancestor (MRCAT) between all pairs of individuals. This information is then used in an algorithm that produces the tree. MRCAT matrices display interesting mathematical properties, which we analyze in detail. We illustrated the method with simulations of a spatial model of speciation based on assortative mating. In the model individuals are separated into males and females, so that both maternal and paternal phylogenetic trees can be generated. The resulting trees were compared with trees inferred from a clustering method based on genetic distances of the same simulated individuals. Phylogenies obtained from simulations can help understand how different speciation processes and model hypothesis affect tree properties. Simulated trees can also be used to test inference methods based on genetic or character distances obtained directly from the final population data, mimicking the process performed for real populations, where the complete past history is inaccessible.

Signatures of Microevolutionary Processes in Phylogenetic Patterns

&NA; Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially‐explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Ecology and Evolution of Species-Rich Interaction Networks

The perception that the complexity of tropical ecological interactions is both a product of evolutionary processes and a feedstock for evolution lies at the origin of Evolutionary Ecology. We now have the opportunity to revisit this foundational perception to gain insight into the processes shaping biodiversity structure and ecosystem functioning. Such an opportunity arises from the ongoing theoretical integration between ecological and evolutionary theories, alongside with the application of the network approach to characterize the structure and dynamics of multi-species communities. In this chapter, we focus on the fundamental aspects of ecological, evolutionary, and eco-evolutionary theories underlying the network approach to the study of multi-species systems, such as megadiverse tropical communities. Together, these perspectives illustrate the challenges we shall face in the decades to come in order to take advantage of ongoing theoretical integration, the gradual accumulation of data on tropical interactions, and the availability of robust analytical and computational tools to enlighten the processes shaping biodiversity.

A genetic approach to the rock-paper-scissors game

Polymorphisms are usually associated with defenses and mating strategies, affecting the individuals fitness. Coexistence of different morphs is, therefore, not expected, since the fittest morph should outcompete the others. Nevertheless, coexistence is observed in many natural systems. For instance, males of the side-blotched lizards (Uta stansburiana) present three morphs with throat colors orange, yellow and blue, which are associated with mating strategies and territorial behavior. The three male morphs compete for females in a system that is well described by the rock-paper-scissors dynamics of game theory. Previous studies have modeled the lizards as hermaphroditic populations whose individuals behavior were determined only by their phenotypes. Here we consider an extension of this dynamical system where diploidy and sexual reproduction are explicitly taken into account. Similarly to the lizards we represent the genetic system by a single locus with three alleles, o, y, and b in a diploid chromosome with dominance of o over y and of y over b. We show that this genotypic description of the dynamics results in the same equilibrium phenotype frequencies as the phenotypic models, but affects the stability of the system, changing the parameter region where coexistence of the three morphs is possible in a rock-paper-scissors game.