Evolutionarily stable strategies of migration in heterogeneous environments

By means of a simulation model we are showing that the rates of migration can be related to avoidance of competition between relatives, especially in clonal organisms. This could result in a strong selective pressure for migration, even at a high cost. In addition, if the habitat is fragmented, migration can strongly affect local dynamics and result in a dramatic decrease of the densities in some places. In parthenogenetically reproducing organisms like aphids, the level of relatedness in local populations is expected to be very high and therefore they can serve as a good model group for testing these hypotheses. This revised version was published online in July 2006 with corrections to the Cover Date.     

Temperature dependence of the free energy landscape of the src-SH3 protein domain

The temperature dependence of the free energy landscape of the src-SH3 protein domain is investigated through fully atomic simulations in explicit solvent. Simulations are performed above and below the folding transition temperature, enabling an analysis of both protein folding and unfolding. The transition state for folding and unfolding, identified from the free energy surfaces, is found to be very similar, with structure in the central hydrophobic sheet and little structure throughout the rest of the protein. This is a result of a polarized folding (unfolding) mechanism involving early formation (late loss) of the central hydrophobic sheet at the transition state. Unfolding simulations map qualitatively well onto low-temperature free energy surfaces but appear, however, to miss important features observed in folding simulations. In particular, details of the folding mechanism involving the opening and closing of the hydrophobic core are not captured by unfolding simulations performed under strongly denaturing conditions. In addition, free energy surfaces at high temperatures do not display a desolvation barrier found at lower temperatures, involving the expulsion of water molecules from the hydrophobic core.     

Evolutionary Landscapes for the Acquisition of New Ligand Recognition by RNA Aptamers

The evolution of ligand specificity underlies many important problems in biology, from the appearance of drug resistant pathogens to the re-engineering of substrate specificity in enzymes. In studying biomolecules, however, the contributions of macromolecular sequence to binding specificity can be obscured by other selection pressures critical to bioactivity. Evolution of ligand specificity in vitro—unconstrained by confounding biological factors—is addressed here using variants of three flavin-binding RNA aptamers. Mutagenized pools based on the three aptamers were combined and allowed to compete during in vitro selection for GMP-binding activity. The sequences of the resulting selection isolates were diverse, even though most were derived from the same flavin-binding parent. Individual GMP aptamers differed from the parental flavin aptamers by 7 to 26 mutations (20 to 57% overall change). Acquisition of GMP recognition coincided with the loss of FAD (flavin-adenine dinucleotide) recognition in all isolates, despite the absence of a counter-selection to remove FAD-binding RNAs. To examine more precisely the proximity of these two activities within a defined sequence space, the complete set of all intermediate sequences between an FAD-binding aptamer and a GMP-binding aptamer were synthesized and assayed for activity. For this set of sequences, we observe a portion of a neutral network for FAD-binding function separated from GMP-binding function by a distance of three mutations. Furthermore, enzymatic probing of these aptamers revealed gross structural remodeling of the RNA coincident with the switch in ligand recognition. The capacity for neutral drift along an FAD-binding network in such close approach to RNAs with GMP-binding activity illustrates the degree of phenotypic buffering available to a set of closely related RNA sequences—defined as the sets functional tolerance for point mutations—and supports neutral evolutionary theory by demonstrating the facility with which a new phenotype becomes accessible as that buffering threshold is crossed.     

Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface

Monte Carlo simulations of molecular recognition at the consensus binding site of the constant fragment (Fc) of human immunoglobulin G (Ig) protein have been performed to analyze structural and thermodynamic aspects of binding for the 13-residue cyclic peptide DCAWHLGELVWCT. The energy landscape analysis of a hot spot at the intermolecular interface using alanine scanning and equilibrium-simulated tempering dynamics with the simplified, knowledge-based energy function has enabled the role of the protein hot spot residues in providing the thermodynamic stability of the native structure to be determined. We have found that hydrophobic interactions between the peptide and the Met-252, Ile-253, His-433, and His-435 protein residues are critical to guarantee the thermodynamic stability of the crystallographic binding mode of the complex. Binding free energy calculations, using a molecular mechanics force field and a solvation energy model, combined with alanine scanning have been conducted to determine the energetic contribution of the protein hot spot residues in binding affinity. The conserved Asn-434, Ser-254, and Tyr-436 protein residues contribute significantly to the binding affinity of the peptide-protein complex, serving as an energetic hot spot at the intermolecular interface. The results suggest that evolutionary conserved hot spot protein residues at the intermolecular interface may be partitioned in fulfilling thermodynamic stability of the native binding mode and contributing to the binding affinity of the complex.     

Patterns of parapatric speciation

Abstract. Geographic variation may ultimately lead to the splitting of a subdivided population into reproductively isolated units in spite of migration. Here, we consider how the waiting time until the first split and its location depend on different evolutionary factors including mutation, migration, random genetic drift, genetic architecture, and the geometric structure of the habitat. We perform large-scale, individual-based simulations using a simple model of reproductive isolation based on a classical view that reproductive isolation evolves as a by-product of genetic divergence. We show that rapid parapatric speciation on the time scale of a few hundred to a few thousand generations is plausible even when neighboring subpopulations exchange several individuals each generation. Divergent selection for local adaptation is not required for rapid speciation. Our results substantiates the claims that species with smaller range sizes (which are characterized by smaller local densities and reduced dispersal ability) should have higher speciation rates. If mutation rate is small, local abundances are low, or substantial genetic changes are required for reproductive isolation, then central populations should be the place where most splits take place. With high mutation rates, high local densities, or with moderate genetic changes sufficient for reproductive isolation, speciation events are expected to involve mainly peripheral populations.     

Canopy Openness Enhances Diversity of Ant–Plant Interactions in the Brazilian Amazon Rain Forest

In closed‐canopy tropical forest understory, light availability is a significant determinant of habitat diversity because canopy structure is highly variable in most tropical forests. Consequently, variation in canopy cover affects the composition and distribution of plant species via creating variable light environments. Nevertheless, little is known about how variation in canopy openness structures patterns of plant–animal interactions. Because of the great diversity and dominance of ants in tropical environments, we used ant–plant interactions as a focal network to evaluate how variation in canopy cover influences patterns of plant–insect interactions in the Brazilian Amazon rain forest. We observed that small increases in canopy openness are associated with increased diversity of ant–plant interactions in our study area, and this change is independent of plant or ant species richness. Additionally, we found smaller niche overlap for both ants and plants associated with greater canopy openness. We hypothesize that enhanced light availability increases the breadth of ant foraging sources because variation in light availability gives rise to plant resources of different quality and amounts. Moreover, greater light availability promotes vegetative growth in plants, creating ant foraging ‘bridges’ between plants. In sum, our results highlight the importance of environmental heterogeneity as a determinant of ant–plant interaction diversity in tropical environments.     

Hidden diversity and endemism on seamounts: focus on poorly dispersive neogastropods

The seamounts chain offers a set of fragmented habitats in which species with poor dispersive ability may undergo divergence in allopatry. Such a scenario may explain the endemism often described on seamounts. In gastropods, it is possible to infer the mode of development of a species from the morphology of its larval shell. Accordingly, we examine the population genetics of several caenogastropods from the Norfolk and Lord Howe seamounts (south‐west Pacific) with contrasting modes of larval development. A prerequisite to our study was to clarify the taxonomic framework. The species delimitation was ruled using an integrative approach, based on both morphological and molecular evidence. Molecular data indicate an unexpected taxonomic diversity within the existing species names. Both the clarification of the taxonomic framework and the importance of the sampling effort allow us to confidently detect cryptic diversity and micro‐endemism. These results are discussed in relation to the dispersive capacities of the organisms. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 420–438.     

Effects of colonization asymmetries on metapopulation persistence

Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity, in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bias in dispersal strength is higher than 25%. Re-colonization patterns that allow for strong local connectivity provide the highest persistence compared to systems that allow circulation. Finally, asymmetry has relatively weak effects when metapopulations maintain strong general connectivity.     

Critical threshold effects of benthiscape structure on stream herbivore movement

In landscape ecology, substantial theoretical progress has been made in understanding how critical threshold levels of habitat loss may result in sudden changes in landscape connectivity to animal movement. Empirical evidence for such thresholds in real systems, however, remains scarce. Streambed landscapes provide a strong testing ground for studying critical thresholds because organisms are faced with substantial environmental heterogeneity while attempting to overcome the physical force of water. In this study, I report on the results from a series of experiments investigating the influence of habitat abundance and current velocity on the movement dynamics of two stream herbivores (caddisfly larva Agapetus boulderensis and snail Physa sp.) that differ substantially in how they perceive landscape structure. Specifically, I ask whether critical thresholds to herbivore movement exist in streambed landscapes. By exploiting the pattern recognition capabilities of artificial neural networks, I found that the rate, sinuosity and directionality of movement by Agapetus and Physa varied nonlinearly according to the abundance of habitat patches, current velocity and habitat-current interaction. Both the study organisms exhibited threshold responses to habitat abundance, yet the location and slope of these thresholds differed between species and with respect to different current velocities. These results suggest that a critical threshold in functional connectivity (i.e. the connection of habitat patches by dispersal) is not an inherent property of the landscape, but in fact emerges from the interplay of species' interactions with landscape structure. Moreover, current velocity interacted with habitat abundance to elicit strong upstream-oriented movement for both the species. This suggests that dispersing individuals may be polarized in the upstream direction and therefore functional connectivity is not equal in all directions. Such results highlight the need for future research addressing the sources of variability of critical threshold effects in ecological phenomena.     

Changes in the distribution of multispecies pest assemblages affect levels of crop damage in warming tropical Andes

Climate induced species range shifts might create novel interactions among species that may outweigh direct climatic effects. In an agricultural context, climate change might alter the intensity of competition or facilitation interactions among pests with, potentially, negative consequences on the levels of damage to crop. This could threaten the productivity of agricultural systems and have negative impacts on food security, but has yet been poorly considered in studies. In this contribution, we constructed and evaluated process‐based species distribution models for three invasive potato pests in the Tropical Andean Region. These three species have been found to co‐occur and interact within the same potato tuber, causing different levels of damage to crop. Our models allowed us to predict the current and future distribution of the species and therefore, to assess how damage to crop might change in the future due to novel interactions. In general, our study revealed the main challenges related to distribution modeling of invasive pests in highly heterogeneous regions. It yielded different results for the three species, both in terms of accuracy and distribution, with one species surviving best at lower altitudes and the other two performing better at higher altitudes. As to future distributions our results suggested that the three species will show different responses to climate change, with one of them expanding to higher altitudes, another contracting its range and the other shifting its distribution to higher altitudes. These changes will result in novel areas of co‐occurrence and hence, interactions of the pests, which will cause different levels of damage to crop. Combining population dynamics and species distribution models that incorporate interspecific trade‐off relationships in different environments revealed a powerful approach to provide predictions about the response of an assemblage of interacting species to future environmental changes and their impact on process rates.