Context-dependent host dispersal and habitat fragmentation determine heterogeneity in infected tick burdens: an agent-based modelling study.

As the incidence of tick-borne diseases has sharply increased over the past decade, with serious consequences for human and animal health, there is a need to identify ecological drivers contributing to heterogeneity in tick-borne disease risk. In particular, the relative importance of animal host dispersal behaviour in its three context-dependent phases of emigration, transfer and settlement is relatively unexplored. We built a spatially explicit agent-based model to investigate how the host dispersal process, in concert with the tick and host demographic processes, habitat fragmentation and the pathogen transmission process, affects infected tick distributions among hosts. A sensitivity analysis explored the impacts of different input parameters on infected tick burdens on hosts and infected tick distributions among hosts. Our simulations indicate that ecological predictors of infected tick burdens differed among the post-egg life stages of ticks, with tick attachment and detachment, tick questing activity and pathogen transmission dynamics identified as key processes, in a coherent way. We also found that the type of host settlement strategy and the proportion of habitat suitable for hosts determined super-spreading of infected ticks. We developed a theoretical mechanistic framework that can serve as a first step towards applied studies of on-the-ground public health intervention strategies.

Roosting ecology of endangered plant-roosting bats on Okinawa Island: Implications for bat-friendly forestry practices.

Roosting information is crucial to guiding bat conservation and bat-friendly forestry practices. The Ryukyu tube-nosed bat Murina ryukyuana (Endangered) and Yanbaru whiskered bat Myotis yanbarensis (Critically Endangered) are forest-dwelling bats endemic to the central Ryukyu Archipelago, Japan. Despite their threatened status, little is known about the roosting ecology of these species and the characteristics of natural maternity roosts are unknown. To inform sustainable forestry practices and conservation management, we radio-tracked day roosts of both species in the subtropical forests of Okinawa's Kunigami Village District. We compared roost and roost site characteristics statistically between M. ryukyuana nonmaternity roosts (males or nonreproductive females), maternity roosts, and all M. yanbarensis roosts. Generalized linear models were used to investigate roost site selection by M. ryukyuana irrespective of sex and age class. Lastly, we compiled data on phenology from this and prior studies. Nonreproductive M. ryukyuana roosted alone and primarily in understory foliage. Murina ryukyuana maternity roosts were limited to stands >50 years old, and ~60% were in foliage. Myotis yanbarensis roosted almost entirely in cavities along gulch bottoms and only in stands >70 years old (~1/3 of Kunigami's total forest area). Murina ryukyuana maternity roosts were higher (4.3 ± 0.6 m) than conspecific nonmaternity roosts (2.3 ± 0.5 m; p < .001) and M. yanbarensis roosts (2.7 ± 0.5 m; not significant). Model results were inconclusive. Both species appear to be obligate plant roosters throughout their life cycle, but the less flexible roosting preferences of M. yanbarensis may explain its striking rarity. To conserve these threatened bats, we recommend the following forestry practices: (a) reduce clearing of understory vegetation, (b) refrain from removing trees along streams, (c) promote greater tree cavity densities by protecting old-growth forests and retaining snags, and (d) refrain from removing trees or understory between April and July, while bats are pupping.

Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago.

The Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species. mtDNA analysis was conducted with 142 DNA remote samples, mostly from faeces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure. Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population. We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among the archipelago's populations. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures.

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers.

We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand,  the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.

How new concepts become universal scientific approaches: insights from citation network analysis of agent-based complex systems science.

Progress in understanding and managing complex systems comprised of decision-making agents, such as cells, organisms, ecosystems or societies, is-like many scientific endeavours-limited by disciplinary boundaries. These boundaries, however, are moving and can actively be made porous or even disappear. To study this process, I advanced an original bibliometric approach based on network analysis to track and understand the development of the model-based science of agent-based complex systems (ACS). I analysed research citations between the two communities devoted to ACS research, namely agent-based (ABM) and individual-based modelling (IBM). Both terms refer to the same approach, yet the former is preferred in engineering and social sciences, while the latter prevails in natural sciences. This situation provided a unique case study for grasping how a new concept evolves distinctly across scientific domains and how to foster convergence into a universal scientific approach. The present analysis based on novel hetero-citation metrics revealed the historical development of ABM and IBM, confirmed their past disjointedness, and detected their progressive merger. The separation between these synonymous disciplines had silently opposed the free flow of knowledge among ACS practitioners and thereby hindered the transfer of methodological advances and the emergence of general systems theories. A surprisingly small number of key publications sparked the ongoing fusion between ABM and IBM research. Beside reviews raising awareness of broad-spectrum issues, generic protocols for model formulation and boundary-transcending inference strategies were critical means of science integration. Accessible broad-spectrum software similarly contributed to this change. From the modelling viewpoint, the discovery of the unification of ABM and IBM demonstrates that a wide variety of systems substantiate the premise of ACS research that microscale behaviours of agents and system-level dynamics are inseparably bound.

Long-term selection using a single trait criterion, non-destructive deformation, in White Leghorns: Effect over time on genetic parameters for traits related to egg production.

Although non-destructive deformation is relevant for assessing eggshell strength, few long-term selection experiments are documented which use non-destructive deformation as a selection criterion. This study used restricted maximum likelihood-based methods with a four-trait animal model to analyze the effect of non-destructive deformation on egg production, egg weight and sexual maturity in a two-way selection experiment involving 17 generations of White Leghorns. In the strong shell line, corresponding to the line selected for low non-destructive deformation values, the heritability estimates were 0.496 for non-destructive deformation, 0.253 for egg production, 0.660 for egg weight and 0.446 for sexual maturity. In the weak shell line, corresponding to the line selected for high non-destructive deformation values, the heritabilities were 0.372, 0.162, 0.703 and 0.404, respectively. An asymmetric response to selection was observed for non-destructive deformation, egg production and sexual maturity, whereas egg weight decreased for both lines. Using non-destructive deformation to select for stronger eggshell had a small negative effect on egg production and sexual maturity, suggesting the need for breeding programs to balance selection between eggshell traits and egg production traits. However, the analysis of the genetic correlation between non-destructive deformation and egg weight revealed that large eggs are not associated with poor eggshell quality.

Spatial Self-Organization of Vegetation Subject to Climatic Stress-Insights from a System Dynamics-Individual-Based Hybrid Model.

In simulation models of populations or communities, individual plants have often been obfuscated in favor of aggregated vegetation. This simplification comes with a loss of biological detail and a smoothing out of the demographic noise engendered by stochastic individual-scale processes and heterogeneities, which is significant among others when studying the viability of small populations facing challenging fluctuating environmental conditions. This consideration has motivated the development of precise plant-centered models. The accuracy gained in the representation of plant biology has then, however, often been balanced by the disappearance in models of important plant-soil interactions (esp. water dynamics) due to the inability of most individual-based frameworks to simulate complex continuous processes. In this study, we used a hybrid modeling approach, namely integrated System Dynamics (SD)-Individual-based (IB), to illustrate the importance of individual plant dynamics to explain spatial self-organization of vegetation in arid environments. We analyzed the behavior of this model under different parameter sets either related to individual plant properties (such as seed dispersal distance and reproductive age) or the environment (such as intensity and yearly distribution of precipitation events). While the results of this work confirmed the prevailing theory on vegetation patterning, they also revealed the importance therein of plant-level processes that cannot be rendered by reaction-diffusion models. Initial spatial distribution of plants, reproductive age, and average seed dispersal distance, by impacting patch size and vegetation aggregation, affected pattern formation and population survival under climatic variations. Besides, changes in precipitation regime altered the demographic structure and spatial organization of vegetation patches by affecting plants differentially depending on their age and biomass. Water availability influenced non-linearly total biomass density. Remarkably, lower precipitation resulted in lower mean plant age yet higher mean individual biomass. Moreover, seasonal variations in rainfall greater than a threshold (here, ±0.45 mm from the 1.3 mm baseline) decreased mean total biomass and generated limit cycles, which, in the case of large variations, were preceded by chaotic demographic and spatial behavior. In some cases, peculiar spatial patterns (e.g., rings) were also engendered. On a technical note, the shortcomings of the present model and the benefit of hybrid modeling for virtual investigations in plant science are discussed.

Effect of Long-Term Selection for Non-Destructive Deformation on Egg Shape in White Leghorns.

Several conventional traits, including eggshell thickness, are commonly being improved genetically as a means to increase eggshell strength. At the same time, researchers have come to recognize that factors related to egg geometry, such as egg shape, are important determinants of the variability remaining in eggshell strength, after conventional traits have been considered. Therefore, given that the value of the egg shape index -the egg's width to length ratio-depends highly on the hen strain, it is necessary to examine the relationship between eggshell strength and shape index more closely in a variety of breeds. From this perspective, by using REML methodology under a five-trait animal model, we analyzed a two-way selection experiment for non-destructive eggshell deformation in 31 generations of White Leghorns, to evaluate the effect of selection for eggshell strength on egg shape. In the strong line, which refers to the line that was selected for decreased non-destructive deformation value, the genetic correlation between eggshell breaking strength and shape index was 0.285±0.055, whereas that between non-destructive deformation and shape index was -0.021±0.063. In the weak line, these values were 0.244±0.055 and -0.093±0.060, respectively. The heritability estimates were 0.381±0.033 for non-destructive deformation, 0.349±0.029 for eggshell breaking strength, and 0.544 ±0.027 for shape index in the strong line, and 0.408±0.031, 0.468±0.032, and 0.484±0.028, respectively, in the weak line. The genetic correlation between eggshell breaking strength and shape index suggests that rounder eggs are somewhat more resistant to breakage than more elongated eggs. The moderately high heritability estimates for shape index indicate the potential to improve egg shape through genetic gain.