Implications of body mass and predation for ape social system and biogeographical distribution

Despite the fact that all African great apes have overlapping diets, they differ substantially in both biogeographical distribution and social organisation: Gorilla lives in relatively small, cohesive groups within a small biogeographical area while Pan is much more widely distributed and lives in large, fluid groups in which the members are rarely all together. In this study we use a modelling approach to identify possible causes and consequences of these differences. We use a time budget model which is based on the relationship between time available for various activities, group size, body mass and climate. We demonstrate the importance of body mass as a critical determinant for maximum ecologically tolerable group size as well as ape distribution patterns. In addition, we show that predation pressure may play a strong role in limiting the distribution of smaller-bodied apes ( Pan ). Predation pressure appears to be especially important if the apes opt for a fission–fusion strategy because it obliges them to maintain larger (sub-) groups. In effect, the apes appear to face a tradeoff between solving the predation problem by increasing body size (at the expense of reduced ecological flexibility) and going for ecological flexibility (but at some cost in terms of how they handle predation).     

How foraging allometries and resource dynamics could explain Bergmann's rule and the body‐size diet relationship in mammals

Two dramatic large scale patterns characterize body size in mammalian herbivores. One is Bergmann's rule that notes that mammals tend to increase in body size at higher latitudes. The other is the inverse relationship between herbivore body size and diet quality. Here, we present a model that may explain both. We start by noting that searching for and handling resources are fundamental activities for feeding mammals. We note that if with body size, encounter probability increases less favorably and handling time more favorably than metabolic costs, then body size represents a tradeoff between search efficiency (favors smaller body size) and handling efficiency (favors larger). If so, then optimal body size increases with both temperature and the conspicuousness of the food, but decreases with food quality. For this to happen there must be food limitation where the herbivores influence food standing crop. Lower energetic foraging costs (lower latitude, lower seasonality and/or higher temperatures) or higher food quality result in lower standing crops of food. A lower standing crop of food favors searching efficiency and, hence, smaller body sizes. Factors that increase the standing crop of food favor handling efficiency and larger body sizes. Simply maximizing net profit from foraging or foraging efficiency that are often assumed to help explain Bergmann's rule do not predict either Bergmann's rule nor the inverse relationship between food quality and body size. With the inclusion of consumer–resource dynamics, fitness maximization predicts both. Testing the model's predictions invites empirical research into the allometries of foraging parameters relating to search and handling.     

Heritability of Batrachochytrium dendrobatidis burden and its genetic correlation with development time in a population of Common toad (Bufo spinosus)

Despite the important threat that emerging pathogens pose for the conservation of biodiversity as well as human health, very little is known about the adaptive potential of host species to withstand infections. We studied the quantitative genetic architecture responsible for the burden of the fungal pathogen Batrachochytrium dendrobatidis in a population of common toads in conjunction with other life‐history traits (i.e., body size and development rate) that may be affected by common selective pressures. We found a significant heritable component that is associated with fungal burden, which may allow for local adaptation to this pathogen to proceed. In addition, the high genetic correlation found between fungal burden and development time suggests that both traits have to be taken into account in order to assess the adaptive response of host populations to this emerging pathogen.     

The immune system as a neural network: a multi-epitope approach.

The term "neural network" has been applied to arrays of simple activation units linked by weighted connections. If the connections are modified according to a defined learning algorithm, such networks can be trained to store and retrieve patterned information. Memories are distributed throughout the network, allowing the network to recall complete patterns from incomplete input (pattern completion). The major biological application of neural network theory to date has been in the neurosciences, but the immune system may represent an alternative organ system in which to search for neural network architecture. Previous applications of parallel distributed processing to idiotype network theory have focused upon the recognition of individual epitopes. We argue here that this approach may be too restrictive, underestimating the power of neural network architecture. We propose that the network stores and retrieves large, complex patterns consisting of multiple epitopes separated in time and space. Such a network would be capable of perceiving an entire bacterium, and of storing the time course of a viral infection. While recognition of solitary epitopes occurs at the cellular level in this model, recognition of structures larger than the width of an antibody binding site takes place at the organ level, via network architecture integration of, i.e. individual epitope responses. The Oudin-Cazenave enigma, the sharing of idiotypic determinants by antibodies directed against distinct regions of the same antigen, suggests that some network level of integration of the individual clonal responses to large antigens does occur. The role of cytokines in prior neural network models of the immune system is unclear. We speculate that cytokines may influence the temperature of the network, such that changes in the cytokine milieu serve to "anneal" the network, allowing it to achieve the optimum steady-state in the shortest period of time.     

Mathematical model of the primary CD8 T cell immune response: stability analysis of a nonlinear age-structured system

The primary CD8 T cell immune response, due to a first encounter with a pathogen, happens in two phases: an expansion phase, with a fast increase of T cell count, followed by a contraction phase. This contraction phase is followed by the generation of memory cells. These latter are specific of the antigen and will allow a faster and stronger response when encountering the antigen for the second time. We propose a nonlinear mathematical model describing the T CD8 immune response to a primary infection, based on three nonlinear ordinary differential equations and one nonlinear age-structured partial differential equation, describing the evolution of CD8 T cell count and pathogen amount. We discuss in particular the roles and relevance of feedback controls that regulate the response. First we reduce our system to a system with a nonlinear differential equation with a distributed delay. We study the existence of two steady states, and we analyze the asymptotic stability of these steady states. Second we study the system with a discrete delay, and analyze global asymptotic stability of steady states. Finally, we show some simulations that we can obtain from the model and confront them to experimental data.     

Extinct or still out there? Disentangling influences on extinction and rediscovery helps to clarify the fate of species on the edge

Each year, two or three species that had been considered to be extinct are rediscovered. Uncertainty about whether or not a species is extinct is common, because rare and highly threatened species are difficult to detect. Biological traits such as body size and range size are expected to be associated with extinction. However, these traits, together with the intensity of search effort, might influence the probability of detection and extinction differently. This makes statistical analysis of extinction and rediscovery challenging. Here, we use a variant of survival analysis known as cure rate modelling to differentiate factors that influence rediscovery from those that influence extinction. We analyse a global data set of 99 mammals that have been categorized as extinct or possibly extinct. We estimate the probability that each of these mammals is still extant and thus estimate the proportion of missing (presumed extinct) mammals that are incorrectly assigned extinction. We find that body mass and population density are predictors of extinction, and body mass and search effort predict rediscovery. In mammals, extinction rate increases with body mass and population density, and these traits act synergistically to greatly elevate extinction rate in large species that also occurred in formerly dense populations. However, when they remain extant, larger‐bodied missing species are rediscovered sooner than smaller species. Greater search effort increases the probability of rediscovery in larger species of missing mammals, but has a minimal effect on small species, which take longer to be rediscovered, if extant. By separating the effects of species characteristics on extinction and detection, and using models with the assumption that a proportion of missing species will never be rediscovered, our new approach provides estimates of extinction probability in species with few observation records and scant ecological information.     

Salamander evolution across a latitudinal cline in gape-limited predation risk

General predictions of community dynamics require that insights derived from local habitats can be scaled up to explain phenomena across geographic scales. Across these larger spatial extents, adaptation can play an increasing role in determining the outcome of species interactions. If local adaptation is common, then our ability to generalize measures of species interaction strength across communities will be limited without an additional understanding of the genetic variation underlying interaction traits. In the context of predator–prey interactions, prey individuals commonly are expected to reduce risky foraging behaviors and subsequent growth under predation threat. However, rapid growth into a large body size can defend against gape-limited predators, creating a tradeoff between increased predation risk due to elevated foraging activity and decreased predation risk due to large size. Here I combine field observations, natural selection experiments, and common garden assays to understand potential adaptations of spotted salamander Ambystoma maculatum larvae to gape-limited and gape-unconstrained predators. Field observations and natural selection trials suggested antagonistic selection on prey body size among ponds dominated by gape-limited predator salamanders A. opacum and gape-unconstrained beetle larvae Dytiscus . In common garden experiments, prey from sites with high gape-limited predation risk grew larger than those from other sites, suggesting the evolution of rapid growth into a prey size refuge. Larvae from all sites grew to a large size when exposed to the gape-limited N. viridescens predator's kairomones. Hence, induced rapid growth into a size refuge may be an adaptive response to gape-limited predation risk. Results point to an important role for cross-community generalizations based on functional classifications of predators by their gape constraints and inter-site genetic variation in prey growth rates and behaviors.     

Epidemic enhancement in partially immune populations

We observe that a pathogen introduced into a population containing individuals with acquired immunity can result in an epidemic longer in duration and/or larger in size than if the pathogen were introduced into a naive population. We call this phenomenon "epidemic enhancement," and use simple dynamical models to show that it is a realistic scenario within the parameter ranges of many common infectious diseases. This finding implies that repeated pathogen introduction or intermediate levels of vaccine coverage can lead to pathogen persistence in populations where extinction would otherwise be expected.     

Habitat disturbance selects against both small and large species across varying climates

Global extinction drivers, including habitat disturbance and climate change, are thought to affect larger species more than smaller species. However, it is unclear if such drivers interact to affect assemblage body size distributions. We asked how these two key global change drivers differentially affect the interspecific size distributions of ants, one of the most abundant and ubiquitous animal groups on earth. We also asked whether there is evidence of synergistic interactions and whether effects are related to species’ trophic roles. We generated a global dataset on ant body size from 333 local ant assemblages collected by the authors across a broad range of climates and in disturbed and undisturbed habitats. We used head length (range: 0.22–4.55 mm) as a surrogate of body size and classified species to trophic groups. We used generalized linear models to test whether body size distributions changed with climate and disturbance, independent of species richness. Our analysis yielded three key results: 1) climate and disturbance showed independent associations with body size; 2) assemblages included more small species in warmer climates and fewer large species in wet climates; and 3) both the largest and smallest species were absent from disturbed ecosystems, with predators most affected in both cases. Our results indicate that temperature, precipitation and disturbance have differing effects on the body size distributions of local communities, with no evidence of synergistic interactions. Further, both large and small predators may be vulnerable to global change, particularly through habitat disturbance.     

Quantifying the effect of colony size and food distribution on harvester ant foraging

Desert seed-harvester ants, genus Pogonomyrmex, are central place foragers that search for resources collectively. We quantify how seed harvesters exploit the spatial distribution of seeds to improve their rate of seed collection. We find that foraging rates are significantly influenced by the clumpiness of experimental seed baits. Colonies collected seeds from larger piles faster than randomly distributed seeds. We developed a method to compare foraging rates on clumped versus random seeds across three Pogonomyrmex species that differ substantially in forager population size. The increase in foraging rate when food was clumped in larger piles was indistinguishable across the three species, suggesting that species with larger colonies are no better than species with smaller colonies at collecting clumped seeds. These findings contradict the theoretical expectation that larger groups are more efficient at exploiting clumped resources, thus contributing to our understanding of the importance of the spatial distribution of food sources and colony size for communication and organization in social insects.     

Isolating Contributions from Intersegmental Transfer to DNA Searching by Alkyladenine DNA Glycosylase

Large genomes pose a challenge to DNA repair pathways because rare sites of damage must be efficiently located from among a vast excess of undamaged sites. Human alkyladenine DNA glycosylase (AAG) employs nonspecific DNA binding interactions and facilitated diffusion to conduct a highly redundant search of adjacent sites. This ensures that every site is searched, but could be a detriment if the protein is trapped in a local segment of DNA. Intersegmental transfer between DNA segments that are transiently in close proximity provides an elegant solution that balances global and local searching processes. It has been difficult to detect intersegmental transfer experimentally; therefore, we developed biochemical assays that allowed us to observe and measure the rates of intersegmental transfer by AAG. AAG has a flexible amino terminus that tunes its affinity for nonspecific DNA, but we find that it is not required for intersegmental transfer. As AAG has only a single DNA binding site, this argues against the bridging model for intersegmental transfer. The rates of intersegmental transfer are strongly dependent on the salt concentration, supporting a jumping mechanism that involves microscopic dissociation and capture by a proximal DNA site. As many DNA-binding proteins have only a single binding site, jumping may be a common mechanism for intersegmental transfer.     

Geographic range size, life history and rates of diversification in Australian mammals

Abstract What causes species richness to vary among different groups of organisms? Two hypotheses are that large geographical ranges and fast life history either reduce extinction rates or raise speciation rates, elevating a clade's rate of diversification. Here we present a comparative analysis of these hypotheses using data on the phylogenetic relationships, geographical ranges and life history of the terrestrial mammal fauna of Australia. By comparing species richness patterns to null models, we show that species are distributed nonrandomly among genera. Using sister‐clade comparisons to control for clade age, we then find that faster diversification is significantly associated with larger geographical ranges and larger litters, but there is no evidence for an effect of body size or age at first breeding on diversification rates. We believe the most likely explanation for these patterns is that larger litters and geographical ranges increase diversification rates because they buffer species from extinction. We also discuss the possibility that positive effects of litter size and range size on diversification rates result from elevated speciation rates.     

Starvation resistance of gypsy moth,Lymantria dispar (L.) (Lepidoptera: Lymantriidae): tradeoffs among growth,body size,and survival

Summary Survival and body composition of starving gypsy moth larvae initially reared on aspen foliage or artificial diet differeing in nitrogen (N) and carbohydrate concentration were examined under laboratory conditions. Diet nitrogen concentration strongly affected starvation resistance and body composition, but diet carbohydrate content had no effects on these. Within any single diet treatment, greater body mass afforded greater resistance to starvation. However, starving larvae reared on 1.5% N diet survived nearly three days longer than larvae reared on 3.5% N diet. Larvae reared on artificial diet survived longer than larvae reared on aspen. Differences in survival of larvae reared on artificial diet with low and high nitrogen concentrations could not be attributed to variation in respiration rates, but were associated with differences in body composition. Although percentage lipid in larvae was unaffected by diet nitrogen concentration, larvae reared on 1.5% N diet had a higher percentage carbohydrate and lower percentage protein in their bodies prior to starvation than larvae reared on 3.5% N diet. Hence, larger energy reserves of larvae reared on low nitrogen diet may have contributed to their greater starvation resistance. Whereas survival under food stress was lower for larvae reared on high N diets, growth rates and pupal weights were higher, suggesting a tradeoff between rapid growth and survival. Larger body size does not necessarily reflect larger energy reserves, and, in fact, larger body size accured via greater protein accumulation may be at the expense of energy reserves. Large, fast-growing larvae may be more fit when food is abundant, but this advantage may be severely diminished under food stress. The potential ecological and evolutionary implications of a growth/survival tradeoff are discussed.     

Multi-Objective Community Detection Based on Memetic Algorithm

Community detection has drawn a lot of attention as it can provide invaluable help in understanding the function and visualizing the structure of networks. Since single objective optimization methods have intrinsic drawbacks to identifying multiple significant community structures, some methods formulate the community detection as multi-objective problems and adopt population-based evolutionary algorithms to obtain multiple community structures. Evolutionary algorithms have strong global search ability, but have difficulty in locating local optima efficiently. In this study, in order to identify multiple significant community structures more effectively, a multi-objective memetic algorithm for community detection is proposed by combining multi-objective evolutionary algorithm with a local search procedure. The local search procedure is designed by addressing three issues. Firstly, nondominated solutions generated by evolutionary operations and solutions in dominant population are set as initial individuals for local search procedure. Then, a new direction vector named as pseudonormal vector is proposed to integrate two objective functions together to form a fitness function. Finally, a network specific local search strategy based on label propagation rule is expanded to search the local optimal solutions efficiently. The extensive experiments on both artificial and real-world networks evaluate the proposed method from three aspects. Firstly, experiments on influence of local search procedure demonstrate that the local search procedure can speed up the convergence to better partitions and make the algorithm more stable. Secondly, comparisons with a set of classic community detection methods illustrate the proposed method can find single partitions effectively. Finally, the method is applied to identify hierarchical structures of networks which are beneficial for analyzing networks in multi-resolution levels.     

Growth, ingestion rates and metabolic activity of walleye in lakes with and without lake herring

Growth efficiencies, ingestions rates and activity levels of walleye Sander vitreus were compared in lakes with and without lake herring Coregonus artedi . Yellow perch Perca flavescens were the main prey in lakes without lake herring. Walleye were sampled in September and October from 38 lakes in Ontario in 1998 and 1999, using multimesh monofilament gillnets. Ingestion rates were estimated from annual increments in somatic mercury and body mass, and the mercury content of yellow perch and lake herring. Walleye had higher growth efficiencies, and lower ingestion and activity rates in lakes with lake herring. Lake herring grow larger than yellow perch and therefore could provide more profitable prey for larger walleye. The results are consistent with optimal foraging theory that predicts that walleye feeding on optimal prey sizes should grow more efficiently, if the ratio of feeding benefit (energy) to cost (search and seizure) is a function of the ratio of predator and prey size.     

Brood size and environmental conditions sex-specifically affect nestling immune response in the European starling Sturnus vulgaris

In sexually size-dimorphic species, the larger sex can be more sensitive to stressful environmental conditions, often resulting in reduced growth and elevated mortality rates. Development of the immune system is regarded as highly resource dependent, and recent data suggest that nestling passerines experience a possible resource-based trade-off between growth and immunity. Given the hypothesized importance of maximizing growth for the larger sex, the corresponding immune system may also exhibit similar sensitivity to limited resources. To better understand how natural variation in brood size and resources might differentially affect growth and immune function in nestlings of a sexually size-dimorphic species, we examined the relationship between brood size and inter-sexual differences in cell-mediated immunity (CMI) and survival in European starling Sturnus vulgaris nestlings where males are larger in both mass and structural size. We hypothesized that male CMI response should be negatively impacted by increasing sibling competition (brood size), especially during periods of low resource availability. In a year of reduced parental provisioning rates and reduced chick growth rates, male offspring exhibited the predicted negative relationship, whereas female CMI response was unaffected. However, in a year of improved provisioning rates and chick growth, neither sex exhibited a negative relationship between immune response and brood size. Thus, natural variation in brood size can affect sex-specific immunity differently in offspring of a sexually size-dimorphic passerine. However, this relationship appears resource-dependent, suggesting that the hypothesized resource-based trade-off may be compensated for in years of adequate resource abundance.     

Global change and carnivore body size: data are stasis

Aim  Global warming and other anthropogenic changes to the environment affect many aspects of biology and have often been invoked as causing body size changes in vertebrates. Here we examine a diverse set of carnivore populations in search of patterns in body size change that could reflect global warming (in accord with Bergmann's rule).
Location  Global.
Methods  We used > 4400 specimens representing 22 carnivore species in 52 populations collected over the last few decades to examine whether size changed with collection date when geography and sex are accounted for. We then examined several factors related to global warming, body mass, diet, and the attributes of the different datasets, to see whether they affect the standardized slope (β) of the size versus time regression.
Results  Six of 52 populations we examined show a significant effect of year of collection on body size at the 0.05 probability level. The response of size to global warming does not reflect spatial patterns of size variation, nor do diet or body mass affect tendency of populations to change in body size. Size changes are no more pronounced in populations that have been sampled more recently. However, change, where it occurs, is rapid.
Main conclusions  There may be a tendency in the literature to report only cases where recent changes are prevalent. Although in our data only a minority of populations show body size changes, we may see changes accelerating in the future in response to more drastic climatic changes and other anthropogenic changes.     

Shifting latitudinal clines in avian body size correlate with global warming in Australian passerines

Intraspecific latitudinal clines in the body size of terrestrial vertebrates, where members of the same species are larger at higher latitudes, are widely interpreted as evidence for natural selection and adaptation to local climate. These clines are predicted to shift in response to climate change. We used museum specimens to measure changes in the body size of eight passerine bird species from south-eastern Australia over approximately the last 100 years. Four species showed significant decreases in body size (1.8–3.6% of wing length) and a shift in latitudinal cline over that period, and a meta-analysis demonstrated a consistent trend across all eight species. Southern high-latitude populations now display the body sizes typical of more northern populations pre-1950, equivalent to a 7° shift in latitude. Using ptilochronology, we found no evidence that these morphological changes were a plastic response to changes in nutrition, a likely non-genetic mechanism for the pattern observed. Our results demonstrate a generalized response by eight avian species to some major environmental change over the last 100 years or so, probably global warming.     

MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing

With the decreasing cost of next-generation sequencing, deep sequencing of clinical samples provides unique opportunities to understand host-associated microbial communities. Among the primary challenges of clinical metagenomic sequencing is the rapid filtering of human reads to survey for pathogens with high specificity and sensitivity. Metagenomes are inherently variable due to different microbes in the samples and their relative abundance, the size and architecture of genomes, and factors such as target DNA amounts in tissue samples (i.e. human DNA versus pathogen DNA concentration). This variation in metagenomes typically manifests in sequencing datasets as low pathogen abundance, a high number of host reads, and the presence of close relatives and complex microbial communities. In addition to these challenges posed by the composition of metagenomes, high numbers of reads generated from high-throughput deep sequencing pose immense computational challenges. Accurate identification of pathogens is confounded by individual reads mapping to multiple different reference genomes due to gene similarity in different taxa present in the community or close relatives in the reference database. Available global and local sequence aligners also vary in sensitivity, specificity, and speed of detection. The efficiency of detection of pathogens in clinical samples is largely dependent on the desired taxonomic resolution of the organisms. We have developed an efficient strategy that identifies “all against all” relationships between sequencing reads and reference genomes. Our approach allows for scaling to large reference databases and then genome reconstruction by aggregating global and local alignments, thus allowing genetic characterization of pathogens at higher taxonomic resolution. These results were consistent with strain level SNP genotyping and bacterial identification from laboratory culture.     

Revising traditional theory on the link between plant body size and fitness under competition: evidence from old‐field vegetation

The selection consequences of competition in plants have been traditionally interpreted based on a “size‐advantage” hypothesis – that is, under intense crowding/competition from neighbors, natural selection generally favors capacity for a relatively large plant body size. However, this conflicts with abundant data, showing that resident species body size distributions are usually strongly right‐skewed at virtually all scales within vegetation. Using surveys within sample plots and a neighbor‐removal experiment, we tested: (1) whether resident species that have a larger maximum potential body size (MAX) generally have more successful local individual recruitment, and thus greater local abundance/density (as predicted by the traditional size‐advantage hypothesis); and (2) whether there is a general between‐species trade‐off relationship between MAX and capacity to produce offspring when body size is severely suppressed by crowding/competition – that is, whether resident species with a larger MAX generally also need to reach a larger minimum reproductive threshold size (MIN) before they can reproduce at all. The results showed that MIN had a positive relationship with MAX across resident species, and local density – as well as local density of just reproductive individuals – was generally greater for species with smaller MIN (and hence smaller MAX). In addition, the cleared neighborhoods of larger target species (which had relatively large MIN) generally had – in the following growing season – a lower ratio of conspecific recruitment within these neighborhoods relative to recruitment of other (i.e., smaller) species (which had generally smaller MIN). These data are consistent with an alternative hypothesis based on a ‘reproductive‐economy‐advantage’ – that is, superior fitness under competition in plants generally requires not larger potential body size, but rather superior capacity to recruit offspring that are in turn capable of producing grand‐offspring – and hence transmitting genes to future generations – despite intense and persistent (cross‐generational) crowding/competition from near neighbors. Selection for the latter is expected to favor relatively small minimum reproductive threshold size and hence – as a tradeoff – relatively small (not large) potential body size.