Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint.     

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

Background  

Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species.     

Classification and evolutionary history of the single-strand annealing proteins,RecT, Redβ, ERF and RAD52

Background  

The DNA single-strand annealing proteins (SSAPs), such as RecT, Redβ, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood.     

Teeth,fossil record and evolutionary history of the cowtail stingray Pastinachus Rüppell, 1829

Abstract

Hypolophin ‘dasyatids’ are a common group of large stingrays today frequenting the Indo-Pacific inshores. Being often harvested in their restricted area, few are known about their biology and their evolutionary history despite a very peculiar dental pattern making it easy to track their fossil record. An abundant material consisting of isolated teeth from Late Bartonian (38–40 Ma) lagoonal deposits of Djebel el Kébar, Tunisia, allows to describe a new stingray, Pastinachus kebarensis nov. sp. This taxon represents the oldest occurrence for this genus but also the oldest fossil record for hypolophins. A dental comparison of these fossils with 3D rendered models of fresh specimens testifies that early hypolophin representatives had already a strongly arcuate and bulbous upper jaw, interlocking with a broad and elongated tooth plate on the lower jaw. This new fossil and its fossil relatives (here updated), indicate a pre-Bartonian origination for hypolophins in western Neotethys, and reveal a rapid and widespread colonization of the proto-Mediterranean Sea, western Atlantic and Indo-Pacific coasts during the late Paleogene–early Neogene. Finally, it is worth noting that early hypolophin representatives seemingly entered freshwater habitats occasionally as modern cowtail stingrays do.     

Dynamics analysis of a predator–prey system with harvesting prey and disease in prey species

In this paper, a predator–prey system with harvesting prey and disease in prey species is given. In the absence of time delay, the existence and stability of all equilibria are investigated. In the presence of time delay, some sufficient conditions of the local stability of the positive equilibrium and the existence of Hopf bifurcation are obtained by analysing the corresponding characteristic equation, and the properties of Hopf bifurcation are given by using the normal form theory and centre manifold theorem. Furthermore, an optimal harvesting policy is investigated by applying the Pontryagin's Maximum Principle. Numerical simulations are performed to support our analytic results.     

Mammalian predator–prey interaction in a fragmented landscape: weasels and voles

The relationship between predators and prey is thought to change due to habitat loss and fragmentation, but patterns regarding the direction of the effect are lacking. The common prediction is that specialized predators, often more dependent on a certain habitat type, should be more vulnerable to habitat loss compared to generalist predators, but actual fragmentation effects are unknown. If a predator is small and vulnerable to predation by other larger predators through intra-guild predation, habitat fragmentation will similarly affect both the prey and the small predator. In this case, the predator is predicted to behave similarly to the prey and avoid open and risky areas. We studied a specialist predator’s, the least weasel, Mustela nivalis nivalis, spacing behavior and hunting efficiency on bank voles, Myodes glareolus, in an experimentally fragmented habitat. The habitat consisted of either one large habitat patch (non-fragmented) or four small habitat patches (fragmented) with the same total area. The study was replicated in summer and autumn during a year with high avian predation risk for both voles and weasels. As predicted, weasels under radio-surveillance killed more voles in the non-fragmented habitat which also provided cover from avian predators during their prey search. However, this was only during autumn, when the killing rate was also generally high due to cold weather. The movement areas were the same for both sexes and both fragmentation treatments, but weasels of both sexes were more prone to take risks in crossing the open matrix in the fragmented treatment. Our results support the hypothesis that habitat fragmentation may increase the persistence of specialist predator and prey populations if predators are limited in the same habitat as their prey and they share the same risk from avian predation.     

Reciprocity in predator–prey interactions: exposure to defended prey and predation risk affects intermediate predator life history and morphology

A vast body of literature exists documenting the morphological, behavioural and life history changes that predators induce in prey. However, little attention has been paid to how these induced changes feed back and affect the predators’ life history and morphology. Larvae of the phantom midge Chaoborus flavicans are intermediate predators in a food web with Daphnia pulex as the basal resource and planktivorous fish as the top predator. C. flavicans prey on D. pulex and are themselves prey for fish; as D. pulex induce morphological defences in the presence of C. flavicans this is an ideal system in which to evaluate the effects of defended prey and top predators on an intermediate consumer. We assessed the impact on C. flavicans life history and morphology of foraging on defended prey while also being exposed to the non-lethal presence of a top fish predator. We tested the basic hypothesis that the effects of defended prey will depend on the presence or absence of top predator predation risk. Feeding rate was significantly reduced and time to pupation was significantly increased by defended morph prey. Gut size, development time, fecundity, egg size and reproductive effort respond to fish chemical cues directly or significantly alter the relationship between a trait and body size. We found no significant interactions between prey morph and the non-lethal presence of a top predator, suggesting that the effects of these two biological factors were additive or singularly independent. Overall it appears that C. flavicans is able to substantially modify several aspects of its biology, and while some changes appear mere consequences of resource limitation others appear facultative in nature.     

Molecular systematics: Perfect SINEs of evolutionary history?

Short interspersed repetitive elements - SINEs - are being championed as near-perfect phylogenetic characters; they have recently been used with notable success to resolve some phylogenetic conundrums, but they do have certain limitations that restrict their use as 'perfect' characters for molecular systematics.     

Insights into the metabolism,lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites'

The archaeal phylum ‘Diapherotrites'' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the ‘Diapherotrites''. The most complete of the SAGs, Candidatus ‘Iainarchaeum andersonii'' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the ‘Diapherotrites'' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. ‘Diapherotrites'' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.     

Influence of edge on predator–prey distribution and abundance

I investigated the effect of spatial configuration on distribution and abundance of invertebrate trophic groups by counting soil arthropods under boxes (21 × 9.5 cm) arranged in six different patterns that varied in the amount of edge (137–305 cm). I predicted fewer individuals from the consumer trophic group (Collembola) in box groups with greater amount of edge. This prediction was based on the assumption that predators (mites, ants, spiders, centipedes) select edge during foraging and thereby reduce abundance of the less mobile consumer group under box patterns with greater edge. Consumer abundance (Collembola) was not correlated with amount of edge. Among the predator groups, mite, ant and centipede abundance related to the amount of edge of box groups. However, in contrast to predictions, abundance of these predators was negatively correlated with amount of edge in box patterns. All Collembola predators, with the exception of ants, were less clumped in distribution than Collembola. The results are inconsistent with the view that predators used box edges to predate the less mobile consumer trophic group. Alternative explanations for the spatial patterns other than predator–prey relations include (1) a negative relationship between edge and moisture, (2) a positive relationship between edge and detritus decomposition (i.e. mycelium as food for the consumer group), and (3) a negative relationship between edge and the interstices between adjacent boxes. Landscape patterns likely affect microclimate, food, and predator–prey relations and, therefore, future experimental designs need to control these factors individually to distinguish among alternative hypotheses.     

Will hotspots conserve extra primate and carnivore evolutionary history?

Setting aside biodiversity hotspots would be especially compelling if they contained not just enormous numbers of species but also excessive evolutionary history. A recent study seemed to provide evidence for this incentive for hotspot conservation. Sechrest et al . (2002 ) reported that hotspots contain more endemic phylogenetic diversity (PD) than expected based on the numbers of primate and carnivore species they contain. We extend their analysis and revise some of their claims. For primates and threatened carnivores, we show that the original analysis was driven by a single hotspot (Madagascar) that contains an ancient endemic clade. The remaining hotspots harbour less rather than significantly more endemic PD than expected. Thus, while one hotspot contains an enormous excess of evolutionary history, the remaining hotspots do not. Our analysis reveals that the overriding influence of a single hotspot can create the misleading impression that hotspots generally contain excessive evolutionary history. Justification for the hotspot initiative should be based on robust evidence. We join others in endorsing an increased role for detailed phylogenetic analysis in conservation planning.     

What determines prey selection in owls? Roles of prey traits,prey class,environmental variables,and taxonomic specialization

Ecological theory suggests that prey size should increase with predator size, but this trend may be masked by other factors affecting prey selection, such as environmental constraints or specific prey preferences of predator species. Owls are an ideal case study for exploring how predator body size affects prey selection in the presence of other factors due to the ease of analyzing their diets from owl pellets and their widespread distributions, allowing interspecific comparisons between variable habitats. Here, we analyze various dimensions of prey resource selection among owls, including prey size, taxonomy (i.e., whether or not particular taxa are favored regardless of their size), and prey traits (movement type, social structure, activity pattern, and diet). We collected pellets of five sympatric owl species (Athene noctua, Tyto alba, Asio otus, Strix aluco, and Bubo bubo) from 78 sites across the Mediterranean Levant. Prey intake was compared between sites, with various environmental variables and owl species as predictors of abundance. Despite significant environmental impacts on prey intake, some key patterns emerge among owl species studied. Owls select prey by predator body size: Larger owls tend to feed on wider ranges of prey sizes, leading to higher means. In addition, guild members show both specialization and generalism in terms of prey taxa, sometimes in contrast with the expectations of the predator–prey body size hypothesis. Our results suggest that while predator body size is an important factor in prey selection, taxon specialization by predator species also has considerable impact.     

Developmental and evolutionary assumptions in a study about the impact of premature birth and low income on mother–infant interaction

In order to study the impact of premature birth and low income on mother–infant interaction, four Portuguese samples were gathered: full-term, middle-class (n = 99); premature, middle-class (n = 63); full-term, low income (n = 22); and premature, low income (n = 21). Infants were filmed in a free play situation with their mothers, and the results were scored using the CARE Index. By means of multinomial regression analysis, social economic status (SES) was found to be the best predictor of maternal sensitivity and infant cooperative behavior within a set of medical and social factors. Contrary to the expectations of the cumulative risk perspective, two factors of risk (premature birth together with low SES) were as negative for mother–infant interaction as low SES solely. In this study, as previous studies have shown, maternal sensitivity and infant cooperative behavior were highly correlated, as was maternal control with infant compliance. Our results further indicate that, when maternal lack of responsiveness is high, the infant displays passive behavior, whereas when the maternal lack of responsiveness is medium, the infant displays difficult behavior. Indeed, our findings suggest that, in these cases, the link between types of maternal and infant interactive behavior is more dependent on the degree of maternal lack of responsiveness than it is on birth status or SES. The results will be discussed under a developmental and evolutionary reasoning.     

Host plant quality,spatial heterogeneity,and the stability of mite predator–prey dynamics

Population dynamics models suggest that both the over-all level of resource productivity and spatial variability in productivity can play important roles in community dynamics. Higher productivity environments are predicted to destabilize consumer–resource dynamics. Conversely, greater heterogeneity in resource productivity is expected to contribute to stability. Yet the importance of these two factors for the dynamics of arthropod communities has been largely overlooked. I manipulated nutrient availability for strawberry plants in a multi-patch experiment, and measured effects of overall plant quality and heterogeneity in plant quality on the stability of interactions between the phytophagous mite Tetranychus urticae and its predator Phytoseiulus persimilis. Plant size, leaf N content and T. urticae population growth increased monotonically with increasing soil nitrogen availability. This gradient in plant quality affected two correlates of mite population stability, population variability over time (i.e., coefficient of variation) and population persistence (i.e., proportion of plant patches colonized). However, the highest level of plant quality did not produce the least stable dynamics, which is inconsistent with the “paradox of enrichment”. Heterogeneity in plant productivity had modest effects on stability, with the only significant difference being less variable T. urticae densities in the heterogeneous compared to the corresponding homogeneous treatment. These results are generally congruent with metapopulation theory and other models for spatially segregated populations, which predict that stability should be governed largely by relative movement rates of predators and prey—rather than patch quality.     

Predicting loss of evolutionary history: Where are we?

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.     

Effects of rapid prey evolution on predator–prey cycles

We study the qualitative properties of population cycles in a predator-prey system where genetic variability allows contemporary rapid evolution of the prey. Previous numerical studies have found that prey evolution in response to changing predation risk can have major quantitative and qualitative effects on predator-prey cycles, including: (1) large increases in cycle period, (2) changes in phase relations (so that predator and prey are cycling exactly out of phase, rather than the classical quarter-period phase lag), and (3) "cryptic" cycles in which total prey density remains nearly constant while predator density and prey traits cycle. Here we focus on a chemostat model motivated by our experimental system (Fussmann et al. in Science 290:1358-1360, 2000; Yoshida et al. in Proc roy Soc Lond B 424:303-306, 2003) with algae (prey) and rotifers (predators), in which the prey exhibit rapid evolution in their level of defense against predation. We show that the effects of rapid prey evolution are robust and general, and furthermore that they occur in a specific but biologically relevant region of parameter space: when traits that greatly reduce predation risk are relatively cheap (in terms of reductions in other fitness components), when there is coexistence between the two prey types and the predator, and when the interaction between predators and undefended prey alone would produce cycles. Because defense has been shown to be inexpensive, even cost-free, in a number of systems (Andersson et al. in Curr Opin Microbiol 2:489-493, 1999: Gagneux et al. in Science 312:1944-1946, 2006; Yoshida et al. in Proc Roy Soc Lond B 271:1947-1953, 2004), our discoveries may well be reproduced in other model systems, and in nature. Finally, some of our key results are extended to a general model in which functional forms for the predation rate and prey birth rate are not specified.     

Structure–function relationship and evolutionary history of the human selenoprotein M (SelM) found over-expressed in hepatocellular carcinoma

In humans we know 25 selenoproteins that play important roles in redox regulation, detoxification, immune-system protection and viral suppression. In particular, selenoprotein M (SelM) may function as thiol disulfide oxidoreductase that participates in the formation of disulfide bonds, and can be implicated in calcium responses. However, it presents a redox motif (CXXU), where U is a selenocysteine, and may also function as redox regulator because its decreased or increased expression regulated by dietary selenium alters redox homeostasis. No data are reported in literature about its involvement in cancer but only in neurodegenerative diseases. In this paper we evaluated the SelM expression in two hepatoma cell lines, HepG2 and Huh7, compared to normal hepatocytes. The results suggested its involvement in hepatocellular carcinoma (HCC) as well as its possible use to follow the progression of this cancer as putative marker. The aim of this study has been to analyze the structure–function relationships of SelM. Hence, firstly we studied the evolutionary history of this protein by phylogenetic analysis and GC content of genes from various species. So, we modeled the three-dimensional structure of the human SelM evaluating its energetic stability by molecular dynamics simulations. Moreover, we modeled some of its mutants to obtain structural information helpful for structure-based drug design.