Proportionate spatial sampling and equal‐time sampling of mobile animals: A dilemma for inferring areal dependence

Abstract Patch or island area is one of the most frequently used variables for inference in conservation biology and biogeography, and is often used in ecological applications. Given that all of these disciplines deal with large spatial scales, exhaustive censusing is not often possible, especially when there are large numbers of patches (e.g. for replication and control purposes). Therefore, data for patches or islands are usually collected by sampling. We argue that if area is to be used as an inferential factor, then the objects under study (i.e. the patches) must be characterized on an areal basis. This necessarily means that fixed‐area sampling is inadequate (e.g. a single standard quadrat or transect set within patches irrespective of the patch area) and that some form of area‐proportionate sampling is needed (e.g. a fixed areal proportion of each patch is surveyed by random allocation of standard quadrats across each patch). However, use of area‐proportionate sampling is not usually dissociated from the increased temporal intensity of sampling that arises from using this approach. The dilemma we see is deciding how much of the area‐specificity of variables such as species richness, rare‐species indices or probabilities of occurrence of individual species is related to the area‐proportionate survey protocol and how much is due to the temporal intensity of surveys. We undertook a study in which we balanced temporal and spatial effects by increasing the time spent surveying smaller patches of vegetation to account for the area‐ratio difference. The estimated species richness of birds of the box–ironbark system of central Victoria, Australia, was found to depend strongly upon area when area‐proportionate sampling alone was performed. When time‐balancing was imposed upon area‐proportionate sampling, the differences between smaller (10‐ha) and larger (40‐ha) areas were much reduced or effectively disappeared. We show that species found in the additional surveys used to conduct the time‐balancing were significantly less abundant than species recorded in area‐proportionate sampling. This effect is probably most severe for mobile animals, but may emerge in other forms of sampling.     

Mice fed on a diet enriched with genetically engineered multivitamin corn show no sub‐acute toxic effects and no sub‐chronic toxicity

Multivitamin corn is a novel genetically engineered variety that simultaneously produces high levels of β‐carotene, ascorbate and folate, and therefore has the potential to address simultaneously multiple micronutrient deficiencies caused by the lack of vitamins A, B9 and C in developing country populations. As part of the development process for genetically engineered crops and following European Food Safety Authority (EFSA) recommendations, multivitamin corn must be tested in whole food/feed sub‐chronic animal feeding studies to ensure there are no adverse effects, and potential allergens must be identified. We carried out a 28‐day toxicity assessment in mice, which showed no short‐term sub‐acute evidence of diet‐related adverse health effects and no difference in clinical markers (food consumption, body weight, organ/tissue weight, haematological and biochemical blood parameters and histopathology) compared to mice fed on a control diet. A subsequent 90‐day sub‐chronic feeding study again showed no indications of toxicity compared to mice fed on control diets. Our data confirm that diets enriched with multivitamin corn have no adverse effects on mice, do not induce any clinical signs of toxicity and do not contain known allergens.     

Water for small‐scale biogas digesters in sub‐Saharan Africa

Biogas could provide a more sustainable energy source than wood fuels for rural households in sub‐Saharan African. However, functioning of biogas digesters can be limited in areas of low water availability. The water required is approximately 50 dm³ day^?1 for each cow and 10 dm³ day^?1 for each pig providing manure to the digester, or 25 (±6) dm³ day^?1 for each person in the household, using a digester volume of 1.3 (±0.3) m³ capita^?1. Here, we consider the potential of domestic water recycling, rainwater harvesting, and aquaculture to supply the water needed for digestion in different countries of sub‐Saharan Africa. Domestic water recycling was found to be important in every country but was usually insufficient to meet the requirements of the digester, with households in 72% of countries need to collect additional water. Rooftop rainwater harvesting also has an important role, iron roofs being more effective than thatched roofs at collecting water. However, even with an iron roof, the size of roof commonly found in sub‐Saharan Africa (15 to 40 m²) is too small to collect sufficient water, requiring an extra area (in m²) for each person of (R/100) (where R is the rainfall in mm). If there is a local market for fish, stocking a pond with tilapia, fed on plankton growing on bioslurry from the digester, could provide an important source of additional income and hold the water required by the digester. In areas where rainfall is low and seasonal, the fishpond might be stocked only in the rainy season, allowing the pond to be covered during the dry period to reduce evaporation. If evaporative losses (E in mm) exceed rainfall, an extra catchment area is needed to maintain the water level in the pond, equivalent to approximately (1.5 × ((E?R)/R)) m² for each person in the household.     

Neuronal sub‐compartmentalization: a strategy to optimize neuronal function

Neurons are highly polarized cells that consist of three main structural and functional domains: a cell body or soma, an axon, and dendrites. These domains contain smaller compartments with essential roles for proper neuronal function, such as the axonal presynaptic boutons and the dendritic postsynaptic spines. The structure and function of these compartments have now been characterized in great detail. Intriguingly, however, in the last decade additional levels of compartmentalization within the axon and the dendrites have been identified, revealing that these structures are much more complex than previously thought. Herein we examine several types of structural and functional sub‐compartmentalization found in neurons of both vertebrates and invertebrates. For example, in mammalian neurons the axonal initial segment functions as a sub‐compartment to initiate the action potential, to select molecules passing into the axon, and to maintain neuronal polarization. Moreover, work in Drosophila melanogaster has shown that two distinct axonal guidance receptors are precisely clustered in adjacent segments of the commissural axons both in vivo and in vitro, suggesting a cell‐intrinsic mechanism underlying the compartmentalized receptor localization. In Caenorhabditis elegans, a subset of interneurons exhibits calcium dynamics that are localized to specific sections of the axon and control the gait of navigation, demonstrating a regulatory role of compartmentalized neuronal activity in behaviour. These findings have led to a number of new questions, which are important for our understanding of neuronal development and function. How are these sub‐compartments established and maintained? What molecular machinery and cellular events are involved? What is their functional significance for the neuron? Here, we reflect on these and other key questions that remain to be addressed in this expanding field of biology.     

Lessons from the Ebola epidemics and their applications for COVID‐19 pandemic response in sub‐Saharan Africa

COVID‐19, caused by a novel coronavirus named SARS‐CoV‐2, was identified in December 2019, in Wuhan, China. It was first confirmed in sub‐Saharan Africa in Nigeria on 27 February 2020 and has since spread quickly to all sub‐Saharan African countries, causing more than 111,309 confirmed cases and 2,498 deaths as of 03 June 2020. The lessons learned during the recent Ebola virus disease (EVD) outbreaks in some sub‐Saharan African countries were expected to shape and influence the region’s responses to COVID‐19 pandemic. However, some of the challenges associated with the management of the EVD outbreaks persist and create obstacles for the effective management of the COVID‐19 pandemic. This article describes the commonalities between the EVD epidemics and COVID‐19 pandemic, with a view to draw on lessons learned to effectively tackle the ongoing pandemic. Key successes, failures and lessons learned from previous EVD outbreaks are discussed. Recommendations on how these lessons can be translated to strengthen the COVID‐19 response in sub‐Saharan Africa are provided.     

Considerations for stakeholder engagement and COVID‐19 related clinical trials’ conduct in sub‐Saharan Africa

The aim of this study is to determine how stakeholder engagement can be adapted for the conduct of COVID‐19‐related clinical trials in sub‐Saharan Africa. Nine essential stakeholder engagement practices were reviewed: formative research; stakeholder engagement plan; communications and issues management plan; protocol development; informed consent process; standard of prevention for vaccine research and standard of care for treatment research; policies on trial‐related physical, psychological, financial, and/or social harms; trial accrual, follow‐up, exit trial closure and results dissemination; and post‐trial access to trial products or procedures. The norms, values, and practices of collectivist societies in Sub‐Saharan Africa and the low research literacy pose challenges to the conduct of clinical trials. Civil‐society organizations, members of community advisory boards and ethics committees, young persons, COVID‐19 survivors, researchers, government, and the private sector are assets for the implementation and translation of COVID‐19 related clinical trials. Adapting ethics guidelines to the socio‐cultural context of the region can facilitate achieving the aim of stakeholder engagement.     

Comparison of two methods for sampling invertebrates: vacuum and sweep‐net sampling

ABSTRACT With numerous invertebrate sampling techniques available, deciding which technique to use under certain circumstances may be difficult. Many researchers interested in invertebrate abundance and availability relative to the foraging ecology of birds may use a technique (e.g., vacuum sampling or sweep‐netting) without understanding the impacts their choice may have on the samples collected and the ability of the method to meet research objectives. We compared the characteristics, including overall biomass, morphospecies richness, average size, diversity, and body length categories, of invertebrates collected using a sweep‐net and a Dietrick vacuum sampler along paired transects in Woodward County, Oklahoma, from May to July 2007 and 2008. These sampling techniques differed in the taxa collected, with the orders Diptera, Homoptera, and Hymenoptera dominating vacuum samples and the orders Homoptera, Orthoptera, and Araneae dominating sweep‐net samples. Although morphospecies richness was similar for the two techniques, the mean size of invertebrates collected and overall invertebrate biomass were greater for sweep‐netting than vacuum sampling. Vacuum sampling was more effective at collecting small (e.g., <5 cm) invertebrates, whereas sweep‐netting captured large (>5 cm) Orthopteran and Lepidopteran larvae at higher rates. Thus, our results indicate that neither sampling method effectively sampled all invertebrate families and investigators should be aware of the potential biases of different sampling techniques and be certain that the technique selected will allow study objectives to be met.     

The Amazonas‐trap: a new method for sampling plant‐inhabiting arthropod communities in tropical forest understory

Methods to quantify plant‐insect interactions in tropical forests may miss many important arthropods and can be time consuming and uneven in capture efficiency. We describe the Amazonas‐trap, a new method that rapidly envelops the target plant for sampling arthropods. We evaluated the efficiency of the Amazonas‐trap by comparing it with two commonly used sampling methods to collect arthropods from plants: the beating tray and manual collection. Samples were collected in 10 permanent plots, in the Ducke forest reserve, Manaus (Amazonas, Brazil). In each plot we sampled 18 plant individuals of Protium sp. (Burseraceae): six by a beating tray, six by manual collection, and six using the Amazonas‐trap. All insects were identified to the family level and those belonging to the order Hymenoptera were identified to the species and morphospecies level. The new method sampled more insect families and more Hymenoptera species than tree beating and manual collection. Of the 75 total families collected, 20 were sampled exclusively by the Amazonas‐trap, seven were only collected with a beating tray, and seven were sampled exclusively with manual collecting. A similar pattern was found for abundance: Amazonas‐trap sampled more individuals, followed by the beating tray and manual collection. Small and winged arthropods were more abundant in Amazonas‐trap, explaining the highest richness of Hymenoptera and insect families sampled with this method. The new method sampled more spiders, wood‐fungi feeders, sap suckers, omnivorous, parasitoids, and insect predators than the other methods, but was equally effective in sampling leaf‐feeders and ants. Amazonas‐trap was more time consuming in the field, but for all diversity parameters evaluated, the new method showed better performance for collecting invertebrates on plants.     

Ethical principles for promoting health research data sharing with sub‐Saharan Africa

A powerful feature of global health research is data‐sharing with regions which bear the heaviest burden of disease. It offers novel opportunities for aggregating data to address critical global health challenges in ways higher than relying on individual studies. Yet there exist important stratifiers of the capacity to share data, particularly across the Global North‐South divide. Systemic challenges that characterize sub‐Saharan Africa and disadvantage the region's scientific productivity threaten the burgeoning data‐sharing culture too. Like all endeavors requiring equal commitments under unequal circumstances, a strong ethical impetus is needed to help reduce inequities and imbalances to encourage adherence. This article discusses mandatory data‐sharing in relation to peculiar challenges faced by sub‐Saharan African scientists to suggest ethical principles for rethinking and reframing solutions. We propose six principles which mirror guidelines from the Institute of Medicine and encapsulate principles from the Emanuel Framework, Nairobi Data Sharing Principles, and the COHRED guidelines.     

Time scale matters: genetic analysis does not support adaptation‐by‐time as the mechanism for adaptive seasonal declines in kokanee reproductive life span

Seasonal declines of fitness‐related traits are often attributed to environmental effects or individual‐level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation‐by‐time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian‐linked loci. We detected no genetic differences in presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation‐by‐time as an important evolutionary mechanism underlying seasonal declines in reproductive life span and a need for greater consideration of other mechanisms such as time‐dependent, adaptive adjustment of reproductive effort.     

genecap: a program for analysis of multilocus genotype data for non‐invasive sampling and capture‐recapture population estimation

We created genecap to facilitate analysis of multilocus genotype data for use in non‐invasive DNA sampling and genetic capture‐recapture studies. genecap is a Microsoft excel macro that uses multilocus genetic data to match samples with identical genotypes, calculate frequency of alleles, identify sample genotypes that differ by one and two alleles, calculate probabilities of identity, and match probabilities for matching samples. genecap allows the user to include background data and samples with missing genotypes for multiple loci. Capture histories for each user‐defined sampling period are output in formats consistent with commonly employed population estimation programs.     

Hotspots of climate change impacts in sub‐Saharan Africa and implications for adaptation and development

Development efforts for poverty reduction and food security in sub‐Saharan Africa will have to consider future climate change impacts. Large uncertainties in climate change impact assessments do not necessarily complicate, but can inform development strategies. The design of development strategies will need to consider the likelihood, strength, and interaction of climate change impacts across biosphere properties. We here explore the spread of climate change impact projections and develop a composite impact measure to identify hotspots of climate change impacts, addressing likelihood and strength of impacts. Overlapping impacts in different biosphere properties (e.g. flooding, yields) will not only claim additional capacity to respond, but will also narrow the options to respond and develop. Regions with severest projected climate change impacts often coincide with regions of high population density and poverty rates. Science and policy need to propose ways of preparing these areas for development under climate change impacts.     

mtDNA variability in two Bantu‐speaking populations (Shona and Hutu) from Eastern Africa: Implications for peopling and migration patterns in sub‐Saharan Africa

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu‐speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu‐speaking populations. Moreover, by comparing our data with those from other Niger‐Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub‐Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu‐speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu‐speaking populations, but also between Bantu and non‐Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu‐speakers, with strong interactions between the different lines of Bantu‐speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Tree dynamics and co‐existence in the montane–sub‐alpine ecotone: the role of different light‐induced strategies

Questions: Is light availability the main factor driving forest dynamics in Pyrenean sub‐alpine forests? Do pines and firs differ in growth, mortality and morphological response to low light availability? Can differences in shade tolerance affect predictions of future biome changes in Pyrenean sub‐alpine forests in the absence of thermal limitation? Location: Montane–sub‐alpine ecotones of the Eastern Pyrenees (NE Spain). Methods: We evaluated morphological plasticity, survival and growth response of saplings of Scots pine, mountain pine and silver fir to light availability in a mixed forest ecotone. For each species, we selected 100 living and 50 dead saplings and measured size, crown morphology and light availability. A wood disk at root collar was then removed for every sapling, and models relating growth and mortality to light were obtained. Results: Fir had the lowest mortality rate (<0.1) for any given light condition. Pines had comparable responses to light availability, although in deep shade Scots pine risked higher mortality (0.35) than mountain pine (0.19). Pines and fir developed opposing strategies to light deprivation: fir employed a conservative strategy based on sacrificing height growth, whereas pines enhanced height growth to escape from shade, but at the expense of higher mortality risk. Scots pine showed higher plasticity than mountain pine for all architectural and morphological traits analysed, having higher adaptive capacity to a changing environment. Conclusions: Our results support the prediction of future biome changes in Pyrenean sub‐alpine forests as silver fir and Scots pine may find appropriate conditions for colonizing mountain pine‐dominated stands due to land‐use change‐related forest densification and climate warming‐related temperature increases, respectively.     

The simultaneous inference of zooplanktivorous fish and macrophyte density from sub‐fossil cladoceran assemblages: a multivariate regression tree approach

1. Quantitative palaeolimnology has traditionally sought to quantify species‐environment relationships to use alterations in biological assemblages to reflect past environmental change. Transfer functions have used regression techniques, such as weighted averaging, to define taxon optima and tolerance for a single chemical or biological variable. 2. Cladoceran assemblages and their sub‐fossil remains in shallow lakes are shaped by a combination of interacting factors. Partial constrained ordination of sub‐fossil cladoceran assemblages from 39 shallow lakes (29 in Norfolk, U.K. and 10 in Denmark) indicated that both zooplanktivorous fish (ZF) density and submerged macrophyte abundance significantly influenced community composition. These dual structuring forces precluded the use of a transfer function as one of the key assumptions of this approach was not met, namely that environmental variables apart from the variable being modelled have negligible influence on species distribution or that there is a linear relationship between the two. Separate transfer functions for ZF and macrophyte abundance were developed but had poor performance diagnostics with low bootstrapped r², high root mean square error of prediction (RMSEP) and large bias. 3. To obviate the problem of multiple structuring forces a multivariate regression tree (MRT) was employed, which allows for more than one explanatory variable within a model. The MRT analysis defined six groups with discrete ranges of ZF and macrophyte densities. The technique identified critical values or ‘break points’ in ZF and macrophyte abundances which result in significant alterations in the sub‐fossil cladoceran assemblage. In addition, the MRT groups had different summer mean values for chlorophyll‐a, Secchi depth, total phosphorus and nitrate‐nitrogen. 4. The predictive abilities of the model were assessed by comparing the observed versus predicted MRT group membership. In general group membership was reliably predicted, suggesting sub‐fossil cladoceran assemblages reliably reflect ZF and macrophyte density in shallow lakes. For a relatively small number of sites there were differences between the observed and predicted MRT group membership. These failures of prediction may result, at least in part, from the disparity of the time period represented by the environmental data and the surface sediment cladoceran assemblage.