Lifetime productivity of dairy cows in smallholder farming systems of the Central highlands of Kenya

Evaluation of lifetime productivity is sensible to target interventions for improving productivity of smallholder dairy systems in the highlands of East Africa, because cows are normally not disposed of based on productive reasons. Feeding strategies and involuntary culling may have long-term effects on productive (and therefore economic) performance of dairy systems. Because of the temporal scale needed to evaluate lifetime productivity, experimentation with feedstuffs in single lactations is not enough to assess improvements in productivity. A dynamic modelling approach was used to explore the effect of feeding strategies on the lifetime productivity of dairy cattle. We used LIVSIM (LIVestock SIMulator), an individual-based, dynamic model in which performance depends on genetic potential of the breed and feeding. We tested the model for the highlands of Central Kenya, and simulated individual animals throughout their lifetime using scenarios with different diets based on common feedstuffs used in these systems (Napier grass, maize stover and dairy concentrates), with and without imposing random mortality on different age classes. The simulations showed that it is possible to maximise lifetime productivity by supplementing concentrates to meet the nutrient requirements of cattle during lactation, and during early development to reduce age at first calving and extend productive life. Avoiding undernutrition during the dry period by supplementing the diet with 0.5 kg of concentrates per day helped to increase productivity and productive life, but in practice farmers may not perceive the immediate economic benefits because the results of this practice are manifested through a cumulative, long-term effect. Survival analyses indicated that unsupplemented diets prolong calving intervals and therefore, reduce lifetime productivity. The simulations with imposed random mortality showed a reduction of 43% to 65% in all productivity indicators. Milk production may be increased on average by 1400 kg per lactation by supplementing the diet with 5 kg of concentrates during early lactation and 1 kg during late lactation, although the optimal supplementation may change according to milk and concentrate prices. Reducing involuntary culling must be included as a key goal when designing interventions to improve productivity and sustainability of smallholder dairy systems, because increasing lifetime productivity may have a larger impact on smallholders’ income than interventions targeted to only improving daily milk yields through feeding strategies.     

Tests for sex-biased dispersal using bi-parentally inherited genetic markers

Understanding why dispersal is sex-biased in many taxa is still a major concern in evolutionary ecology. Dispersal tends to be male-biased in mammals and female-biased in birds, but counter-examples exist and little is known about sex bias in other taxa. Obtaining accurate measures of dispersal in the field remains a problem. Here we describe and compare several methods for detecting sex-biased dispersal using bi-parentally inherited, codominant genetic markers. If gene flow is restricted among populations, then the genotype of an individual tells something about its origin. Provided that dispersal occurs at the juvenile stage and that sampling is carried out on adults, genotypes sampled from the dispersing sex should on average be less likely (compared to genotypes from the philopatric sex) in the population in which they were sampled. The dispersing sex should be less genetically structured and should present a larger heterozygote deficit. In this study we use computer simulations and a permutation test on four statistics to investigate the conditions under which sex-biased dispersal can be detected. Two tests emerge as fairly powerful. We present results concerning the optimal sampling strategy (varying number of samples, individuals, loci per individual and level of polymorphism) under different amounts of dispersal for each sex. These tests for biases in dispersal are also appropriate for any attribute (e.g. size, colour, status) suspected to influence the probability of dispersal. A windows program carrying out these tests can be freely downloaded from http://www.unil.ch/izea/softwares/fstat.html     

Physiological integration affects growth form and competitive ability in clonal plants

Clonal plants translocate resources through spacers between ramets. Translocation can be advantageous if a plant occurs in heterogeneous environments (division of labour); however, because plants interact locally, any spatial arrangement of ramets generates some heterogeneity in light and nutrients even if there is no external heterogeneity. Thus the capacity of a clonal plant to exploit heterogeneous environment must operate in an environment where heterogeneity is partly shaped by the plant growth itself. Since most experiments use only simple systems of two connected ramets, plant-level effects of translocation are unknown. A spatially explicit simulation model of clonal plant growth, competition and translocation is used to identify whether different patterns of translocation have the potential to affect the growth form of the plant and its competitive ability. The results show that different arrangements of translocation sinks over the spacer system can completely alter clonal morphology. Both runners and clumpers can be generated using the same architectural rules by changing translocation only. The effect of translocation strongly interacts with the architectural rules of the plant growth: plants with ramets staying alive when a spacer is formed are much less sensitive to change in translocation than plants with ramets only at the tip. If translocation cost is low, translocating plants are in most cases better competitors than plants that do not translocate; the difference becomes stronger in more productive environments. Key traits that confer competitive ability are total number of ramet, and their fine-scale aggregation.Co-ordinating editor: J. Tuomi     

A Theoretical Study of River Fragmentation by Dams and its Effects on White Sturgeon Populations

Most of the world's large rivers are fragmented by dams. Fragmentation of the river ecosystem alters migration patterns among fish populations and converts free-flowing river to reservoir habitat. In this study, we used an individual-based genetic metapopulation model to study the effects of fragmentation on the population viability and genetic diversity of a large-river fish, the white sturgeon, Acipenser transmontanus. In the first of two simulation experiments, we fragmented a 200km river reach by building 1 to 20 virtual dams. Increased fragmentation produced an exponential decline in the likelihood of persistence, but no extinction threshold to suggest a minimum viable length of river. Compounding isolation with the loss of free-flowing habitat did not further reduce viability until free-flowing habitat was nearly eliminated, at which point extinction was certain. Genetic diversity within (among) populations decreased (increased) as we built the first several dams. Adding more dams caused the number of persisting populations to decline and eroded genetic diversity within and among populations. Our second simulation experiment evaluated the effects of different levels of upstream and downstream migration between river segments. The results of these migration experiments highlighted the importance of balanced migration rates. We found that extinction risk was high for populations linked by high downstream, and low upstream, migration rates, as is often the case in impounded rivers. Our results support the view that migration patterns will play a significant role in determining the viability of riverine fishes, such as the white sturgeon, in river ecosystems fragmented by dams.(retired)     

General response patterns of fish populations to stress: an evaluation using an individual-based simulation model

General response patterns of fish populations tostress, originally proposed by Colby for fisheriesrehabilitation and later adapted by Munkittrick forcontaminants, were evaluated using an individual-basedsimulation model. General response patterns relatechanges in population-level variables to the type ofstress. The model follows the daily growth,mortality, and spawning of individual yellow perch andwalleye through their lifetime, and was corroboratedusing Oneida Lake data. Two versions of the model wereused: population (yellow perch only) and community(dynamic predation on yellow perch by walleye). Eightstresses were imposed on the population and communityversions of the model and 100-year simulations wereperformed. Response patterns were defined by changesin predicted yellow perch mean population abundance,mean age of adults, and mean adult growth (representedby mean length at age-7). Proposed response patternswere similar to those predicted using the populationversion of the model. Simulations using the communityversion of the model distorted the response patterns,either causing amplification, dampening, or reversalof many of the patterns. Predicted response patternsbecame unique when additional variables were included.Our model results suggest that caution is appropriatein interpreting general response patterns based onmean age, or when the population of interest plays amajor role in a relatively simple food web. The responsepattern approach may be better at identifying the lifestage impacted rather than the mechanism of the stress.     

Spatial competition with Lactococcus lactis in mixed-species continuous-flow biofilms inhibits Listeria monocytogenes growth

Surfaces in industrial settings provide a home for resident biofilms that are likely to interact with the attachment, growth and survival of pathogens such as Listeria monocytogenes. Experimental results have indicated that L. monocytogenes cells were inhibited by the presence of a model resident flora (Lactococcus lactis) in dual-species continuous flow-biofilms, and are spatially restricted to the lower biofilm layers. Using a new, simplified individual-based model (IBM) that simulates bacterial cell growth in a three-dimensional space, the spatial arrangements of the two species were reconstructed and their cell counts successfully predicted. This model showed that the difference in generation times between L. monocytogenes and L. lactis cells during the initial stages of dual-species biofilm formation was probably responsible for the species spatialization observed and the subsequent inhibition of growth of the pathogen.     

Intertwined effects of defaunation,increased tree mortality and density compensation on seed dispersal

Contemporary defaunation has profound ecological consequences ranging from local or even global co-extinctions of interacting species to the loss of ecosystem functions and services critical for humanity. Other components of global change (climate change, introduced pests, land use changes) are also harming ecosystem functioning by augmenting tree mortality worldwide. Defaunation and increased tree mortality often coincide in many human-altered ecosystems but whether they interact, leading to non-additive effects on ecosystem functioning, remains largely unknown. However, under some ecological circumstances, the decline or extirpation of one species due to defaunation can be neutralized by increases in the abundance of some functionally similar species (i.e. ‘density compensation’). We combined long-term field data with individual-based modelling to investigate the potential interactive effects of seed disperser loss, increased tree mortality and density compensation on seed dispersal in a heterogeneous landscape. Our simulation experiments showed that both stressors markedly limit not only the quantity of seed dispersal but also its quality since the impact on seed dispersal strongly varied among habitat types that differ strikingly in suitability for tree establishment. Density compensation had a marked positive effect on seed dispersal which, however, was largely limited under increased tree mortality. The combined negative effects of defaunation and increased tree mortality on seed dispersal were lower than the expected additive effect. This highlights the need to account for the joint operation of multiple stressors to accurately predict the impacts of global change on the link between biodiversity and ecosystem functioning.     

From theory to practice in pattern-oriented modelling: identifying and using empirical patterns in predictive models

To robustly predict the effects of disturbance and ecosystem changes on species, it is necessary to produce structurally realistic models with high predictive power and flexibility. To ensure that these models reflect the natural conditions necessary for reliable prediction, models must be informed and tested using relevant empirical observations. Pattern-oriented modelling (POM) offers a systematic framework for employing empirical patterns throughout the modelling process and has been coupled with complex systems modelling, such as in agent-based models (ABMs). However, while the production of ABMs has been rising rapidly, the explicit use of POM has not increased. Challenges with identifying patterns and an absence of specific guidelines on how to implement empirical observations may limit the accessibility of POM and lead to the production of models which lack a systematic consideration of reality. This review serves to provide guidance on how to identify and apply patterns following a POM approach in ABMs (POM-ABMs), specifically addressing: where in the ecological hierarchy can we find patterns; what kinds of patterns are useful; how should simulations and observations be compared; and when in the modelling cycle are patterns used? The guidance and examples provided herein are intended to encourage the application of POM and inspire efficient identification and implementation of patterns for both new and experienced modellers alike. Additionally, by generalising patterns found especially useful for POM-ABM development, these guidelines provide practical help for the identification of data gaps and guide the collection of observations useful for the development and verification of predictive models. Improving the accessibility and explicitness of POM could facilitate the production of robust and structurally realistic models in the ecological community, contributing to the advancement of predictive ecology at large.