A faecal index of diet quality that predicts reproductive success in a marsupial folivore

Estimating the nutritional value of a herbivore’s diet is difficult because it requires knowing what the animal eats, the relative quality of each component and how these components interact in relation to animal physiology. Current methods are cumbersome and rely on many assumptions that are hard to evaluate. We describe a new method for estimating relative diet quality directly from faeces that avoids the problems inherent in other methods. We combine this method with near infrared reflectance spectroscopy (NIRS) to analyse many samples and thus provide a technique with immense value in ecological studies. The method stems from the correlation between the concentrations of dietary and faecal nitrogen in herbivores eating a tannin-free diet, but a weaker relationship in browsers that ingest substantial amounts of tannins, which form complexes with proteins. These complexes reduce the availability of nitrogen and may increase faecal nitrogen concentrations. Using the tannin-binding compound, polyethylene glycol, we showed that tannin-bound nitrogen is a significant and variable part of faecal nitrogen in wild common brushtail possums (Trichosurus vulpecula). We developed a technique to measure faecal available nitrogen and found that it predicted the reproductive success of female brushtail possums in northern Australia. Faecal available nitrogen combined with NIRS provides a powerful tool for estimating the relative nutritional value of the diets of browsing herbivores in many ecological systems. It is a better indicator of diet quality than other commonly used single-nutrient measures such as faecal nitrogen and foliage analysis paired with observed feeding behaviour.     

Aphid (Hemiptera: Aphidoidea) diversity in Tunisia in relation to seed potato production

Winged morphs of aphids were investigated from 2002 to 2004 in 4 Tunisian regions of potato seeds production in order to know the aphid diversity and the potential vectors of Potato Virus Y. This is a very important contribution to the knowledge of aphid fauna in Maghreb. A total of 50,030 aphids were caught using yellow water traps and one suction trap. 130 taxa were identified including 103 species. Ten species are well represented in all regions prospected and typical species were also observed in every region. Some differences in species diversity appeared between regions which are discussed considering weather condition and vegetation.     

Partitioning of genetic variation across the genome using multimarker methods in a wild bird population

The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.     

The Effect of Nonindependent Mate Pairing on the Effective Population Size

The effective population size (N_e) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for N_e typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, including humans. To explore the effects on N_e of nonindependent mate pairing across breeding events, we simulated the genetic drift of mitochondrial DNA, autosomal DNA, and sex chromosome DNA under three mating systems. Nonindependent mate pairing across breeding seasons has no effect when all adults mate pair for life, a small or moderate effect when females reuse stored sperm, and a large effect when there is intense male–male competition for reproduction in a harem social system. If adult females reproduce at a constant rate irrespective of the type of mate pairing, the general effect of nonindependent mate pairing is to decrease N_e for paternally inherited components of the genome. These findings have significant implications for the relative N_e values of different genomic regions, and hence for the expected levels of DNA sequence diversity in these regions.THE effective population size (N_e) is a fundamental parameter of population genetics, which quantifies the effect of genetic drift, the stochastic change in allele frequencies over time in a population of finite size (Wright 1931). The magnitude of N_e affects both the level of genetic variability within a population and the efficiency with which populations retain mildly beneficial mutations and purge mildly deleterious ones. This influences a myriad of genetic phenomena, such as the level of DNA sequence polymorphism, the rate of substitution of nonsynonymous and functional noncoding nucleotide positions, the abundance of transposable elements, levels of variation, and the rate of evolution of gene expression, the persistence of duplicate genes, and genome size and organization (Lynch 2007; Charlesworth 2009). There are a variety of definitions of N_e; here we use the definition in terms of the mean coalescence time of a pair of neutral alleles, which is given by 2N_e (Charlesworth 2009). This definition has the useful feature that the expected pairwise nucleotide site diversity under the widely used infinite sites model is equal to 4N_eμ, where μ is the neutral mutation rate (Kimura 1971).As a result of differences in their ploidy level and mode of inheritance, autosomal DNA (aDNA), the X chromosome (xDNA), the Y chromosome (yDNA), and maternally transmitted organelle DNA such as mitochondrial DNA (mtDNA) generally have a different N_e values. Under certain conditions, such as constant population size, discrete generations, a Poisson distribution of reproductive success, and a sex ratio equal to one, the relative N_e values of these genomic regions (N_e-a, N_e-x, N_e-mt, and N_e-y) are expected to be 4:3:1:1 (Charlesworth 2009). This is because aDNA is biparentally inherited and diploid; xDNA is biparentally inherited, diploid in females, and haploid in males (with female heterogamety, the reverse applies to the Z chromosome), and yDNA (the W chromosome, with female heterogamety) and mtDNA are both effectively uniparentally inherited and haploid in most species.However, several characteristics of natural populations, such as unequal numbers of males and females and nonrandom variation in reproductive success, can affect the value of N_e, even for populations with discrete generations (reviewed in Caballero 1994; Hedrick 2007; Charlesworth 2009). In addition, natural selection at sites linked to neutral markers also has the potential to increase N_e (under balancing selection) (Charlesworth 2006) or to decrease N_e (with background selection or selective sweeps) (Hudson and Kaplan 1988; Charlesworth et al. 1993). Because the nature of natural selection varies in different genomic regions, especially in relation to the rate of recombination, N_e may also vary among unlinked regions with the same ploidy and mode of inheritance, for example, different portions of an autosomal chromosome (Gossmann et al. 2011). In natural populations, these factors can skew the relative N_e values away from the 4:3:1:1 expectation. Even when the effects of natural selection and “nonideal” demography are ignored, the 4:3:1:1 relation still has a large variance when applied to individual loci (Hudson and Turelli 2003).When generations overlap, an additional source of possible deviations from these idealized relations arises from variation among individuals in survival and reproductive success among breeding seasons (Felsenstein 1971; Hill 1972, 1979; Johnson 1977) and from sex differences in demographic parameters and stochastic changes in population size (Engen et al. 2007). In contrast, the effect of a high variance in reproductive success caused by male–male competition is lessened when generations overlap for many breeding seasons (Nunney 1993; Charlesworth 2001). Conversely, overlapping generations with nonindependent mate pairing across breeding seasons could increase the variance in reproductive success. For example, in humans, paternity is correlated with paternal confidence in paternity (Anderson 2006), and married individuals tend to repeatedly produce offspring with each other more frequently than expected by chance. Nonindependent mate pairing among breeding seasons occurs in many other species as well—for example, long-term pair bonding in prairie voles (DeVries et al. 1995), harems in gorillas (Gatti et al. 2004), and sperm storage in fruit flies (Neubaum and Wolfner 1999).Current theoretical models that allow calculation of the effective population size with overlapping generations and age structure make several simplifying assumptions, notably constant sizes of each age class, sufficiently large numbers of individuals in each age class that second-order terms in their reciprocals can be neglected, and independent sampling of offspring genotypes from the same individual reproducing at different times (Hill 1972; Nunney 1991, 1993; Caballero 1994; Charlesworth 1994, 2001). The latter assumption in particular makes it difficult to provide accurate expressions for species such as humans and Drosophila, which reproduce nonindependently because of long-term pair bonds and sperm storage, respectively (Charlesworth 2001).The goal of this study is therefore to explore the consequences of nonindependence of reproductive events across time in different social systems and with different age structures, using simulations of genetic drift in two types of age-structured populations, under different scenarios of independent and nonindependent mate pairing among breeding events. We have explored how these scenarios affect the relative values of N_e-a, N_e-x, N_e-mt, and N_e-y using the infinite alleles model of mutation (Kimura and Crow 1964), with particular emphasis on comparisons of similar mating systems that differ in the extent of nonindependence among breeding events.     

Volatile Exchange between Undamaged Plants - a New Mechanism Affecting Insect Orientation in Intercropping

Changes in plant volatile emission can be induced by exposure to volatiles from neighbouring insect-attacked plants. However, plants are also exposed to volatiles from unattacked neighbours, and the consequences of this have not been explored. We investigated whether volatile exchange between undamaged plants affects volatile emission and plant-insect interaction. Consistently greater quantities of two terpenoids were found in the headspace of potato previously exposed to volatiles from undamaged onion plants identified by mass spectrometry. Using live plants and synthetic blends mimicking exposed and unexposed potato, we tested the olfactory response of winged aphids, Myzus persicae. The altered potato volatile profile deterred aphids in laboratory experiments. Further, we show that growing potato together with onion in the field reduces the abundance of winged, host-seeking aphids. Our study broadens the ecological significance of the phenomenon; volatiles carry not only information on whether or not neighbouring plants are under attack, but also information on the emitter plants themselves. In this way responding plants could obtain information on whether the neighbouring plant is a competitive threat and can accordingly adjust their growth towards it. We interpret this as a response in the process of adaptation towards neighbouring plants. Furthermore, these physiological changes in the responding plants have significant ecological impact, as behaviour of aphids was affected. Since herbivore host plants are potentially under constant exposure to these volatiles, our study has major implications for the understanding of how mechanisms within plant communities affect insects. This knowledge could be used to improve plant protection and increase scientific understanding of communication between plants and its impact on other organisms.     

Effects of X-Ray Dose On Rhizosphere Studies Using X-Ray Computed Tomography

X-ray Computed Tomography (CT) is a non-destructive imaging technique originally designed for diagnostic medicine, which was adopted for rhizosphere and soil science applications in the early 1980s. X-ray CT enables researchers to simultaneously visualise and quantify the heterogeneous soil matrix of mineral grains, organic matter, air-filled pores and water-filled pores. Additionally, X-ray CT allows visualisation of plant roots in situ without the need for traditional invasive methods such as root washing. However, one routinely unreported aspect of X-ray CT is the potential effect of X-ray dose on the soil-borne microorganisms and plants in rhizosphere investigations. Here we aimed to i) highlight the need for more consistent reporting of X-ray CT parameters for dose to sample, ii) to provide an overview of previously reported impacts of X-rays on soil microorganisms and plant roots and iii) present new data investigating the response of plant roots and microbial communities to X-ray exposure. Fewer than 5% of the 126 publications included in the literature review contained sufficient information to calculate dose and only 2.4% of the publications explicitly state an estimate of dose received by each sample. We conducted a study involving rice roots growing in soil, observing no significant difference between the numbers of root tips, root volume and total root length in scanned versus unscanned samples. In parallel, a soil microbe experiment scanning samples over a total of 24 weeks observed no significant difference between the scanned and unscanned microbial biomass values. We conclude from the literature review and our own experiments that X-ray CT does not impact plant growth or soil microbial populations when employing a low level of dose (<30 Gy). However, the call for higher throughput X-ray CT means that doses that biological samples receive are likely to increase and thus should be closely monitored.     

The Long Term Economic Impact of Severe Obstetric Complications for Women and Their Children in Burkina Faso

This study investigates the long term economic impact of severe obstetric complications for women and their children in Burkina Faso, focusing on measures of food security, expenditures and related quality of life measures. It uses a hospital based cohort, first visited in 2004/2005 and followed up four years later. This cohort of 1014 women consisted of two main groups of comparison: 677 women who had an uncomplicated delivery and 337 women who experienced a severe obstetric complication which would have almost certainly caused death had they not received hospital care (labelled a “near miss” event). To analyze the impact of such near miss events as well as the possible interaction with the pregnancy outcome, we compared household and individual level indicators between women without a near miss event and women with a near miss event who either had a live birth, a perinatal death or an early pregnancy loss. We used propensity score matching to remove initial selection bias. Although we found limited effects for the whole group of near miss women, the results indicated negative impacts: a) for near miss women with a live birth, on child development and education, on relatively expensive food consumption and on women’s quality of life; b) for near miss women with perinatal death, on relatively expensive foods consumption and children’s education and c) for near miss women who had an early pregnancy loss, on overall food security. Our results showed that severe obstetric complications have long lasting consequences for different groups of women and their children and highlighted the need for carefully targeted interventions.