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Feeding poultry with live insect larvae stimulates natural behaviour and improves poultry welfare, when poultry has prolonged or frequent access to the larvae. But how to feed live insect larvae to poultry without labour-intensive hand feeding? This paper focusses on the development of a device that overcomes this challenge. A circular device was designed with eight storage compartments, which were filled once a day with live Black Soldier Fly (BSF) larvae (Hermetia illucens). A motor controlled the timed rotation of the device multiple times per day, initiating the release of larvae when a compartment was pushed over an outlet. Every 60 minutes, a new compartment was pushed over the outlet, which means that after eight hours all compartments are emptied. To achieve a gradual release of larvae per storage compartment the device was timed to move every 30 minutes half a storage compartment forward. The larval release was recorded every 5 minutes within the 60 minutes. The device was tested at 18 °C, 24 °C and 30 °C, with 3.4 g and 129.8 g BSF larvae per compartment, and with three different outlet types of different size and shape. The larval release rate was influenced by temperature, amount of larvae, outlet type, and interactions between these factors. After placing a new compartment above the outlet, 50% of the larvae were on average released within 6 minutes. After 60 minutes, on average only 0.5% larvae remained in the compartment. Outlets with wider openings are preferred over the outlet with the narrowest outlet because less larvae remained in the compartments. The dispenser fulfilled the low-labour-intensity requirement as filling was only necessary once a day, the release of different amounts of larvae was achieved over several hours. This automatic dispenser provides a valuable tool to investigate the behaviour of poultry fed with live BSF larvae.

In this repository there are R scripts and dataset to reproduce results and figures from our paper and Supplementary Material.

Protein (P) and carbohydrate (C) concentrations present in food affect larval performance, larval body nutrient concentration, and fecundity of the black soldier fly (BSF). We substantially expanded the range of dietary P- and C-concentrations investigated thus far to assess the effects of nutritionally – unbalanced diets on BSF larval and adult life-history traits, and on larval body protein and lipid concentrations. Twenty five artificial diets varying in their P- and C-concentration and ratio were formulated. We tested five macronutrient (P+C) concentrations (5, 15, 25, 50 and 75%) and five P:C ratios (1:1, 1:2, 1:4, 2:1 and 4:1). BSF performance was affected by P+C-concentration rather than by P:C ratios. A P-concentration between 10 and 15% and a C-concentration between 10 and 60% supported high larval and adult performance. P-concentration is limiting for most of the performance variables, however, a P-concentration higher than 37% reduced larval survival. C-concentration affected egg production more strongly than P-concentration. Overall, at P+C values of 25 and 50%, and P:C ratios 1:2 and 1:4 resulted in the highest values of most of the larval and adult performance variables we measured. For the protein and carbohydrate sources tested, dietary macronutrient concentrations significantly affected larval and adult performance of BSF in different ways. These results show a remarkable degree of nutritional plasticity, and point to the relevance of differentiating the formulation of diets to achieve maximal larval yield, high body protein or high body lipid accumulation or high adult emergence and egg production.

Gastrointestinal helminth-microbiota associations are shaped by various ecological processes. The effect of the ecological context of the host on the bacterial microbiome and gastrointestinal helminth parasites has been tested in a number of ecosystems and experimentally. This study takes the important step to look at these two groups at the same time and to start to examine how these communities interact in a changing host environment. Fresh faecal samples (N = 335) from eight wild Eulemur populations were collected over 2 years across Madagascar. We used 16S ribosomal RNA gene sequencing to characterise the bacterial microbiota composition, and faecal flotation to isolate and morphologically identify nematode eggs. Infections with nematodes of the genera Callistoura and Lemuricola occurred in all lemur populations. Seasonality significantly contributed to the observed variation in microbiota composition, especially in the dry deciduous forest. Microbial richness and Lemuricola spp. infection prevalence were highest in a previously intensely logged site, whereas Callistoura spp. showed no such pattern. In addition, we observed significant correlations between gastrointestinal parasites and bacterial microbiota composition in these lemurs, with 0.4–0.7% of the variation in faecal bacterial microbiota composition being explained by helminth infections. With this study, we show effects of environmental conditions on gastrointestinal nematodes and bacterial interactions in wild lemurs and believe it is essential to consider the potential role of microbiome-parasite associations on the hosts’ GI stability, health, and survival.

Under sexual selection, mate preferences can evolve for traits advertising fitness benefits. Observed mating patterns (mate choice) are often assumed to represent preference, even though they result from the interaction between preference, sampling strategy and environmental factors. Correlating fitness with mate choice instead of preference will therefore lead to confounded conclusions about the role of preference in sexual selection. Here we show that direct fitness benefits underlie mate preferences for genetic characteristics in a unique experiment on wild great tits. In repeated mate preference tests, both sexes preferred mates that had similar heterozygosity levels to themselves, and not those with which they would optimise offspring heterozygosity. In a subsequent field experiment where we cross fostered offspring, foster parents with more similar heterozygosity levels had higher reproductive success, despite the absence of assortative mating patterns. These results support the idea that selection for preference persists despite constraints on mate choice.

Background and aims: Organic inputs have a positive effect on the soil organic matter balance. They are therefore an important asset for soil fertility and crop growth. This study quantifies the additional yield effect due to organic inputs for arable crops in Europe when macro-nutrients are not a limiting factor. Methods: A meta-analysis was performed using data from 20 long-term experiments in Europe. Maxima of yield response curves to nitrogen were compared, with and without organic inputs, under abundant P and K supply. Results: We were surprised to find that, across all experiments, the mean additional yield effect of organic inputs was not significant (+ 1.4 % ± 1.6 (95 % confidence interval)). In specific cases however, especially for root and tuber crops, spring sown cereals, or for very sandy soils or wet climates, organic inputs did increase attainable yields. A significant correlation was found between increase in attainable yields and increase in soil organic matter content. Conclusions: Aggregating data from 20 long-term experiments in Europe, this study shows that organic inputs and/or soil organic matter do not necessarily increase yields, given sufficient nutrients are supplied by mineral fertilisers. Results show the relevance of some environmental factors for additional yield effect of organic inputs, but no simple relation between organic inputs and crop growth.

Background Bat flies (Streblidae and Nycteribiidae) are among the most specialized families of the order Diptera. Members of these two related families have an obligate ectoparasitic lifestyle on bats, and they are known disease vectors for their hosts. However, bat flies have their own ectoparasites: fungi of the order Laboulbeniales. In Europe, members of the Nycteribiidae are parasitized by four species belonging to the genus Arthrorhynchus. We carried out a systematic survey of the distribution and fungus-bat fly associations of the genus in central Europe (Hungary, Romania). Results We encountered the bat fly Nycteribia pedicularia and the fungus Arthrorhynchus eucampsipodae as new country records for Hungary. The following bat-bat fly associations are for the first time reported: Nycteribia kolenatii on Miniopterus schreibersii, Myotis blythii, Myotis capaccinii and Rhinolophus ferrumequinum; Penicillidia conspicua on Myotis daubentonii; and Phthiridium biarticulatum on Myotis capaccinii. Laboulbeniales infections were found on 45 of 1,494 screened bat flies (3.0%). We report two fungal species: Arthrorhynchus eucampsipodae on Nycteribia schmidlii, and A. nycteribiae on N. schmidlii, Penicillidia conspicua, and P. dufourii. Penicillidia conspicua was infected with Laboulbeniales most frequently (25%, n = 152), followed by N. schmidlii (3.1%, n = 159) and P. dufourii (2.0%, n = 102). Laboulbeniales seem to prefer female bat fly hosts to males. We think this might be due to a combination of factors: female bat flies have a longer life span, while during pregnancy female bat flies are significantly larger than males and accumulate an excess of fat reserves. Finally, ribosomal DNA sequences for A. nycteribiae are presented. Conclusions We screened ectoparasitic bat flies from Hungary and Romania for the presence of ectoparasitic Laboulbeniales fungi. Arthrorhynchus eucampsipodae and A. nycteribiae were found on three species of bat flies. This study extends geogra

Soil biota are responsible for essential ecosystem services such as carbon storage, nutrient cycling and water retention. However, assessment of the condition of soil biota is hampered by an overwhelming level of diversity. With representatives in all trophic levels of the food web, nematode communities can be used as bio-indicators. Accurate assessment of nematode assemblages requires insight in the distribution of specimens with distinct food preferences. With the availability of taxon-specific quantitative-PCR assays, distribution patterns of multiple nematode groups can be investigated simultaneously. Here, microscale patchiness of 45 nematode taxa was studied on 12 sampling sites (each with four adjacent microplots) located on arable fields or semi-natural grasslands (‘system’), and on marine-, river clay or sandy soils (‘soil type’). From each microplot five composite samples were collected. Contrary to our expectations, an increase of the number of cores per composite sample did not result in more accurate measurements, and apparently the levels of microscale patchiness of the taxa are low compared to what has been reported for oligophagous plant-parasites. System and soil type did not affect microscale distribution. To investigate the level of patchiness in more detail, detection probability (DP) and variability of abundances were calculated. Common and widespread bacterivorous and fungivorous taxa had DP ≥ 90%, confirming low level of microscale patchiness. With DPs of 40-70%, predators and most omnivores showed degrees of local clustering. An overview of mean variabilities of abundances is presented that offers insight in how feeding preferences impact the microscale distribution both between and within trophic groups.

Habitats in the Wadden Sea, a world heritage area, are affected by land subsidence resulting from naturalgas extraction and by sea level rise. Here we describe a method to monitor changes in habitat types byproducing sequential maps based on point information followed by mapping using a multinomial logitregression model with abiotic variables of which maps are available as predictors.In a 70 ha study area a total of 904 vegetation samples has been collected in seven sampling roundswith an interval of 2–3 years. Half of the vegetation plots was permanent, violating the assumptionof independent data in multinomial logistic regression. This paper shows how this dependency can beaccounted for by adding a random effect to the multinomial logit (MLN) model, thus becoming a mixedmultinomial logit (MMNL) model. In principle all regression coefficients can be taken as random, butin this study only the intercepts are treated as location-specific random variables (random interceptsmodel). With six habitat types we have five intercepts, so that the number of extra model parametersbecomes 15, 5 variances and 10 covariances.The likelihood ratio test showed that the MMNL model fitted significantly better than the MNL modelwith the same fixed effects. McFadden-R2for the MMNL model was 0.467, versus 0.395 for the MNL model.The estimated coefficients of the MMNL and MNL model were comparable; those of altitude, the mostimportant predictor, differed most. The MMNL model accounts for pseudo-replication at the permanentplots, which explains the larger standard errors of the MMNL coefficients. The habitat type at a givenlocation-year combination was predicted by the habitat type with the largest predicted probability. Theseries of maps shows local trends in habitat types most likely driven by sea-level rise, soil subsidence,and a restoration project.We conclude that in environmental modeling of categorical variables using panel data, dependencyof repeated observations at permanent plots

Our olfactory sense plays an important role in eating behavior by modulating our food preferencesand intake. However, hunger or satiety may also influence how we perceive odors. Albeitspeculative, contradictory results found in the past may have resulted from confounding by typeof meal that participants ate to induce satiety. We aimed to investigate the influence of hunger stateon olfactory sensitivity, comparing hunger to satiety using 2 different types of lunch to controlfor sensory-specific satiety. Odor detection thresholds were measured in 2 groups of participants(39 per group, 18–40 years), under 3 conditions: when hungry (twice), after a sweet lunch, andafter a savory lunch. One group had their detection thresholds tested for a sweet odor, whereasin the other group, sensitivity to a savory odor was measured. Differences in olfactory sensitivityconditions were analyzed using linear mixed models. Participants had higher scores on the odorsensitivity task in a hungry versus satiated state (P = 0.001). Within the satiated condition, there wasno effect of type of lunch on odor sensitivity. In conclusion, hunger slightly enhances sensitivityto food odors, but did not significantly depend on the type of food participants ate, suggesting noclear influence of sensory-specific satiety.

Background Chrysomela populi (poplar leaf beetle) is a common herbivore in poplar plantations whose infestation causes major economic losses. Because plant volatiles act as infochemicals, we tested whether isoprene, the main volatile organic compound (VOC) produced by poplars (Populus x canescens), affects the performance of C. populi employing isoprene emitting (IE) and transgenic isoprene non-emitting (NE) plants. Our hypothesis was that isoprene is sensed and affects beetle orientation or that the lack of isoprene affects plant VOC profiles and metabolome with consequences for C. populi feeding. Results Electroantennographic analysis revealed that C. populi can detect higher terpenes, but not isoprene. In accordance to the inability to detect isoprene, C. populi showed no clear preference for IE or NE poplar genotypes in the choice experiments, however, the beetles consumed a little bit less leaf mass and laid fewer eggs on NE poplar trees in field experiments. Slight differences in the profiles of volatile terpenoids between IE and NE genotypes were detected by gas chromatography - mass spectrometry. Non-targeted metabolomics analysis by Fourier Transform Ion Cyclotron Resonance Mass Spectrometer revealed genotype-, time- and herbivore feeding-dependent metabolic changes both in the infested and adjacent undamaged leaves under field conditions. Conclusions We show for the first time that C. populi is unable to sense isoprene. The detected minor differences in insect feeding in choice experiments and field bioassays may be related to the revealed changes in leaf volatile emission and metabolite composition between the IE and NE poplars. Overall our results indicate that lacking isoprene emission is of minor importance for C. populi herbivory under natural conditions, and that the lack of isoprene is not expected to change the economic losses in poplar plantations caused by C. populi infestation.

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Apart from relatively well-studied aboveground effects, invasive plant species will also impact the soil food web. So far, most research has been focusing on primary decomposers, while studies on effects at higher trophic levels are relatively scarce. Giant goldenrod Solidago gigantea, native to North America, is a widespread and common invasive species in most European countries. We investigated its impact on plant communities and on multiple trophic levels of the soil food web in two contrasting habitats: riparian zones and semi-natural grasslands. In 30 pairs of invaded and uninvaded plots, floristic composition, pH, fungal biomass and the densities of 11 nematode taxa were determined by using a quantitative PCR-based method. In the two habitats, the invader outcompeted both rare and dominant plant species. Belowground, S. gigantea invasion reduced pH, increased overall fungal biomass as well as the density of a single lineage of fungivorous nematodes, the family Aphelenchoididae. The densities of two other, phylogenetically distinct lineages of fungivorous nematodes, Aphelenchidae and Diphtherophoridae, were unaffected by the local increase in fungal biomass. Apparently this plant species induces a local asymmetric boost of the fungal community, and only Aphelenchoididae were able to benefit from this invader-induced change. The alternative explanation - the results are explained by a subtle, S. gigantea - induced 0.1-0.2 units decrease of pH - seems unlikely, as pH optima for nematode taxa are relatively broad. Thus, apart from readily observable aboveground effects, the invasive plant species S. gigantea affects fungal biomass as well as a specific part of the fungivorous nematode community in a soil type-independent manner. [KEYWORDS: EXOTIC PLANT INVASIONS NEMATODE COMMUNITIES ALIEN PLANTS ERGOSTEROL BIOTA DIVERSITY BIODIVERSITY EXTRACTION CANADENSIS FEEDBACKS], Apart from relatively well-studied aboveground effects, invasive plant species will also impact the soil food web. So far, most research has been focusing on primary decomposers, while studies on effects at higher trophic levels are relatively scarce. Giant goldenrod Solidago gigantea, native to North America, is a widespread and common invasive species in most European countries. We investigated its impact on plant communities and on multiple trophic levels of the soil food web in two contrasting habitats: riparian zones and semi-natural grasslands. In 30 pairs of invaded and uninvaded plots, floristic composition, pH, fungal biomass and the densities of 11 nematode taxa were determined by using a quantitative PCR-based method. In the two habitats, the invader outcompeted both rare and dominant plant species. Belowground, S. gigantea invasion reduced pH, increased overall fungal biomass as well as the density of a single lineage of fungivorous nematodes, the family Aphelenchoididae. The densities of two other, phylogenetically distinct lineages of fungivorous nematodes, Aphelenchidae and Diphtherophoridae, were unaffected by the local increase in fungal biomass. Apparently this plant species induces a local asymmetric boost of the fungal community, and only Aphelenchoididae were able to benefit from this invader-induced change. The alternative explanation - the results are explained by a subtle, S. gigantea - induced 0.1-0.2 units decrease of pH - seems unlikely, as pH optima for nematode taxa are relatively broad. Thus, apart from readily observable aboveground effects, the invasive plant species S. gigantea affects fungal biomass as well as a specific part of the fungivorous nematode community in a soil type-independent manner. [KEYWORDS: EXOTIC PLANT INVASIONS NEMATODE COMMUNITIES ALIEN PLANTS ERGOSTEROL BIOTA DIVERSITY BIODIVERSITY EXTRACTION CANADENSIS FEEDBACKS]

Dietary protein and salt affect the concentration of milk urea nitrogen (MUN; mg of N/dL) and the relationship between MUN and excretion of urea nitrogen in urine (UUN; g of N/d) of dairy cattle. The aim of the present study was to examine the effects of dietary protein and sodium chloride (NaCl) intake separately, and their interaction, on MUN and UUN, on the relationship between UUN and MUN, on renal recycling of urea, and on urea transfer to the gastrointestinal tract. Twelve second-parity cows (body weight of 645±37kg, 146±29d in milk, and a milk production of 34.0±3.28kg/d), of which 8 were previously fitted with a rumen cannula, were fitted with catheters in the urine bladder and jugular vein. The experiment had a split-plot arrangement with dietary crude protein (CP) content as the main plot factor [116 and 154g of CP/kg of dry matter (DM)] and dietary NaCl content as the subplot factor (3.1 and 13.5g of Na/kg of DM). Cows were fed at 95% of the average ad libitum feed intake of cows receiving the low protein diets. Average MUN and UUN were, respectively, 3.90mg of N/dL and 45g of N/d higher for the high protein diets compared with the low protein diets. Compared with the low NaCl diets, MUN was, on average, 1.74mg of N/dL lower for the high NaCl diets, whereas UUN was unaffected. We found no interaction between dietary content of protein and NaCl on performance characteristics or on MUN, UUN, urine production, and renal clearance characteristics. The creatinine clearance rate was not affected by dietary content of protein and NaCl. Urea transfer to the gastrointestinal tract, expressed as a fraction of plasma urea entry rate, was negatively related to dietary protein, whereas it was not affected by dietary NaCl content. We found no interaction between dietary protein and NaCl content on plasma urea entry rate and gastrointestinal urea entry rate or their ratio. The relationship between MUN and UUN was significantly affected by the class variable dietary NaCl

Fish larvae experience many environmental challenges during development such as variation in water velocity, food availability and predation. The rapid development of structures involved in feeding, respiration and swimming increases the chance of survival. It has been hypothesized that mechanical loading induced by muscle forces plays a role in prioritizing the development of these structures. Mechanical loading by muscle forces has been shown to affect larval and embryonic bone development in vertebrates, but these investigations were limited to the appendicular skeleton. To explore the role of mechanical load during chondrogenesis and osteogenesis of the cranial, axial and appendicular skeleton, we subjected zebrafish larvae to swim-training, which increases physical exercise levels and presumably also mechanical loads, from 5 until 14 days post fertilization. Here we show that an increased swimming activity accelerated growth, chondrogenesis and osteogenesis during larval development in zebrafish. Interestingly, swim-training accelerated both perichondral and intramembranous ossification. Furthermore, swim-training prioritized the formation of cartilage and bone structures in the head and tail region as well as the formation of elements in the anal and dorsal fins. This suggests that an increased swimming activity prioritized the development of structures which play an important role in swimming and thereby increasing the chance of survival in an environment where water velocity increases. Our study is the first to show that already during early zebrafish larval development, skeletal tissue in the cranial, axial and appendicular skeleton is competent to respond to swim-training due to increased water velocities. It demonstrates that changes in water flow conditions can result into significant spatio-temporal changes in skeletogenesis., Fish larvae experience many environmental challenges during development such as variation in water velocity, food availability and predation. The rapid development of structures involved in feeding, respiration and swimming increases the chance of survival. It has been hypothesized that mechanical loading induced by muscle forces plays a role in prioritizing the development of these structures. Mechanical loading by muscle forces has been shown to affect larval and embryonic bone development in vertebrates, but these investigations were limited to the appendicular skeleton. To explore the role of mechanical load during chondrogenesis and osteogenesis of the cranial, axial and appendicular skeleton, we subjected zebrafish larvae to swim-training, which increases physical exercise levels and presumably also mechanical loads, from 5 until 14 days post fertilization. Here we show that an increased swimming activity accelerated growth, chondrogenesis and osteogenesis during larval development in zebrafish. Interestingly, swim-training accelerated both perichondral and intramembranous ossification. Furthermore, swim-training prioritized the formation of cartilage and bone structures in the head and tail region as well as the formation of elements in the anal and dorsal fins. This suggests that an increased swimming activity prioritized the development of structures which play an important role in swimming and thereby increasing the chance of survival in an environment where water velocity increases. Our study is the first to show that already during early zebrafish larval development, skeletal tissue in the cranial, axial and appendicular skeleton is competent to respond to swim-training due to increased water velocities. It demonstrates that changes in water flow conditions can result into significant spatio-temporal changes in skeletogenesis.

In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel or microcapillary system. The profiles are usually interpreted as binary band absence/presence patterns. We focus on two major problems: (1) Within a profile two or more fragments of the same length but of different genomic origin may have been selected, colliding into a single band. This collision problem, akin to the birthday problem, may be surprisingly large. (2) In a pair of profiles two equally long fragments of different genomic origin may have been selected, appearing as identical bands in the two profiles. This is called homoplasy. Both problems are quantified by modeling AFLP as a random sampling technique of fragment lengths. AFLP may be used in phylogenetic studies to estimate the pairwise genetic similarity of individuals. Similarity coefficients like Dice and Jaccard coefficients overestimate the true genetic similarity because of homoplasy, with increasing bias for higher numbers of bands per profile. Corrected estimators are described, which do not suffer from bias. The ideas are illustrated using a new software tool. Data from studies on Arabidopsis and tomato serve as examples. Finally, we make some recommendations with respect to the use of AFLP.

Milk urea nitrogen (MUN; mg of N/dL) has been shown to be related to excretion of urinary urea N (UUN; g of N/d) and total excretion of urinary N (UN; g of N/d) in dairy cows. In the present experiment, it was hypothesized that MUN and the relationship between MUN and UUN or UN is affected by urine volume as a result of dietary sodium chloride intake. Twelve lactating Holstein-Friesian dairy cows (mean ± SD: milk production 28.1 ± 3.23 kg/d and 190 ± 41 d in milk), of which 4 were fitted with catheters in the urine bladder and jugular vein, were randomly assigned to 4 dietary levels of sodium chloride (3, 9, 14, and 19 g of Na/kg of DM) according to a triple 4 × 4 Latin square design. Cows were fed at 95% of ad libitum intake, excluding salt addition. Milk was analyzed for MUN and protein content; urine was analyzed for total N, urea, and creatinine content; feces were analyzed for total N and DM content; and blood plasma was analyzed for urea and creatinine content. Creatinine clearance rate (CCR; L/min) and renal urea reabsorption ratio were estimated based on plasma concentrations of urea and creatinine, and total excretion of urea and creatinine in urine. Intake of DM and N, milk production, and milk protein content were (mean ± SD), on average, 21.4 ± 1.24 kg/d, 522 ± 32.0 g/d, 25.4 ± 2.53 kg/d, and 3.64 ± 0.186%, respectively. A linear relationship was found between Na intake and urine production [urine (kg/d; mean ± SE) = 7.5 ± 4.33 + 0.136 ± 0.0143 × Na intake (g/d)] and between Na intake and MUN [MUN (mg/dL; mean ± SE) = 13.5 ± 0.35 - 0.0068 ± 0.00104 × Na intake (g/d)]. Despite the decrease in MUN with increased Na intake, UN excretion increased linearly with Na intake. Excretion of UUN was not affected by dietary Na content. A linear plateau relationship was observed between CCR and renal urea reabsorption. An increase in CCR coincided with an increase in calculated renal urea reabsorption until a CCR breakpoint value (mean ± SD) of 1.56 ± 0.063 L/min was

Females of the larval parasitoid of Drosophila, Asobara citri, from sub-Saharan Africa, defend patches with hosts by fighting and chasing conspecific females upon encounter. Females of the closely related, palearctic species Asobara tabida do not defend patches and often search simultaneously in the same patch. The effect of patch defence by A. citri females on their distribution in a multi-patch environment was investigated, and their distributions were compared with those of A. tabida. For both species 20 females were released from two release-points in replicate experiments. Females of A. citri quickly reached a regular distribution across 16 patches, with a small variance/mean ratio per patch. Conversely, A. tabida females initially showed a clumped distribution, and after gradual dispersion, a more Poisson-like distribution across patches resulted (variance/mean ratio was closer to 1 and higher than for A. citri). The dispersion of A. tabida was most probably an effect of exploitation: these parasitoids increasingly made shorter visits to already exploited patches. We briefly discuss hypotheses on the adaptive significance of patch defence behaviour or its absence in the light of differences in the natural history of both parasitoid species, notably the spatial distribution of their hosts.

Background: Automated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex). Results: We present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence. Conclusions: We have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy- Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www. plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.

AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary system, and are separated by length, with shorter fragments traveling further. Multiple individuals are simultaneously fingerprinted on a gel. One of the applications of AFLP is the estimation of genetic similarity between individuals, e.g. in diversity and phylogenetic studies. In that case, profiles of two individuals are compared, and the fraction of shared (comigrating) bands is calculated, e.g. using the Dice similarity coefficient. Two comigrating bands may share the same fragment, but band sharing could also be due to chance, if two equally sized, but different fragments are amplified. This is called homoplasy. Homoplasy biases similarity coefficients. Homoplasy could also occur within a lane, if two different fragments of equal length are amplified, resulting in a single band. We call this collision. The main objective of this thesis is the study of collision and homoplasy in AFLP. The length distribution of AFLP fragments plays an important role. This distribution is highly skewed with more abundant short fragments. By simulation the expected similarity for unrelated genotypes is calculated. As much as 40% of the bands may be shared by chance in case of profiles with 120 bands. The collision problem is analogous to the birthday problem, which has a surprising solution. The collision problem is even more extreme, making it even more surprising. Profiles with only 19 bands contain collision(s) with probability 1/2. These findings have consequences for practice. In some cases it is better to prevent the occurrence of collisions by decreasing the number of bands, in other cases a correction for homoplasy and collision is preferred. Modified similarity coefficients are p

Background - Posterior mapping is an increasingly popular hierarchical Bayesian based method used to infer character histories and reconstruct ancestral states at nodes of molecular phylogenies, notably of morphological characters. As for all Bayesian analyses specification of prior values is an integrative and important part of the analysis. He we provide an example of how alternative prior choices can seriously influence results and mislead interpretations. Methods/Principal Findings - For two contrasting discrete morphological characters, namely a slow and a fast evolving character found in the plant family Annonaceae, we specified a total of eight different prior distributions per character. We investigated how these prior settings affected important summary statistics. Our analyses showed that the different prior distributions had marked effects on the results in terms of average number of character state changes. These differences arise because priors play a crucial role in determining which areas of parameter space the values of the simulation will be drawn from, independent of the data at hand. However, priors seemed to fit the data better if they would result in a more even sampling of parameter space (normal posterior distribution), in which case alternative standard deviation values had little effect on the results. The most probable character history for each character was affected differently by the prior. For the slower evolving character, the same character history always had the highest posterior probability independent of the priors used. In contrast, the faster evolving character showed different most probable character histories depending on the prior. These differences could be related to the level of homoplasy exhibited by each character. Conclusions - Although our analyses were restricted to two morphological characters within a single family, our results underline the importance of carefully choosing prior values for posterior mapping. Prior s

A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics.

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce

Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results - In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from

Within the Dutch genomics initiative the ¿Centre for Biosystems Genomics¿ (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies

The gene (Cbg) encoding cortisol-binding globulin (CBG) has been proposed as a candidate gene to explain genetic variation in cortisol secretion and carcass composition in pigs. The objective of this study was to evaluate the association between CBG and pork quality in 5 European breeding lines, Pietrain, Large White (LW), and Landrace purebred lines, a Duroc synthetic line, and a Meishan (MS) x LW advanced intercross. Cortisol-binding globulin maximum binding capacity (CBG-Bmax) was twice as high (P <0.05) in MS x LW pigs compared with the other lines. There was no (P > or = 0.364) association between CBG-Bmax and carcass quality traits in Pietrain gilts, but CBG-Bmax was associated with increased loin yields in LW (P = 0.010) and Landrace (P = 0.103) gilts, decreased ham yields (P = 0.082) in Duroc gilts, and increased fat depth (P = 0.064) and leaf fat (P = 0.001) in MS x LW gilts. There was no association between CBG-Bmax and pork quality traits in Pietrain (P > or = 0.269) and Duroc (P > or = 0.114) gilts. Conversely, CBG-Bmax was associated with lighter (higher L* values; P <0.05) pork in Land-race gilts, as well as lower (P

To understand evolution of foraging behaviour in the whitefly parasitoid Encarsia formosa (Hymenoptera, Aphelinidae), natural densities and distributions of whitefly (Homoptera, Aleyrodidae) were quantified in E. formosa's presumed area of origin, the Neotropics. Leaves were collected in Costa Rican nature areas along long transects (2-4 km), short transects (100 m), within 3-D plots (50 dm32.3 m3) and along suspension bridges within the canopy, and checked for presence of whitefly nymphs. Generalised linear mixed modelling revealed that the number of hosts on the lower side of a leaflet of an average plant within an average spot of an average transect could be described by a Poisson distribution with mean and variance equal to 0.241, in a ratio of I1:I2:I3:I4 = 0.14:0.23:0.26:0.37. The Poisson mean was affected largely by the plant and less by the spot or transect. Variation in leaf area explained little of the variation between plants. Based on the shape of the opening in vacate Semivariance analyses showed that in one of the three short transects, the numbers of whiteflies on leaves were spatially dependent. In four of seven 3-D plots at least one level of spatial dependence could be detected. Results are discussed in the context of understanding evolution of foraging behaviour by E. formosa. [KEYWORDS: Aleyrodidae Encarsia formosa ; foraging behaviour; Homoptera host ; density host distribution ; natural history Neotropics ; parasitoid whitefly], To understand evolution of foraging behaviour in the whitefly parasitoid Encarsia formosa (Hymenoptera, Aphelinidae), natural densities and distributions of whitefly (Homoptera, Aleyrodidae) were quantified in E. formosa's presumed area of origin, the Neotropics. Leaves were collected in Costa Rican nature areas along long transects (2-4 km), short transects (100 m), within 3-D plots (50 dm32.3 m3) and along suspension bridges within the canopy, and checked for presence of whitefly nymphs. Generalised linear mixed modelling revealed that the number of hosts on the lower side of a leaflet of an average plant within an average spot of an average transect could be described by a Poisson distribution with mean and variance equal to 0.241, in a ratio of I1:I2:I3:I4 = 0.14:0.23:0.26:0.37. The Poisson mean was affected largely by the plant and less by the spot or transect. Variation in leaf area explained little of the variation between plants. Based on the shape of the opening in vacate Semivariance analyses showed that in one of the three short transects, the numbers of whiteflies on leaves were spatially dependent. In four of seven 3-D plots at least one level of spatial dependence could be detected. Results are discussed in the context of understanding evolution of foraging behaviour by E. formosa. [KEYWORDS: Aleyrodidae Encarsia formosa ; foraging behaviour; Homoptera host ; density host distribution ; natural history Neotropics ; parasitoid whitefly]

Remotely sensed images are increasingly being used for collection of spatial information. A wide development in sensor systems has occurred during the last decades, resulting in improved spatial, temporal, and spectral resolution. The collection of data by remote sensing is generally more efficient and cheaper than by direct observation and measurement on the ground, although still of a varying quality. Data collected by sensors may be affected by atmospheric factors between sensors and the values reflected on the earth's surface, local impurities on the earth's surface, technical deficiencies of sensors and other factors. In addition, only the reflection of the sensor's signal or of the sunlight on the earth's surface is being measured, and no direct measurements are made. Consequently, the quality of maps produced by remote sensing needs to be assessed.

Remotely sensed images are increasingly being used for collection of spatial information. A wide development in sensor systems has occurred during the last decades, resulting in improved spatial, temporal, and spectral resolution. The collection of data by remote sensing is generally more efficient and cheaper than by direct observation and measurement on the ground, although still of a varying quality. Data collected by sensors may be affected by atmospheric factors between sensors and the values reflected on the earth's surface, local impurities on the earth's surface, technical deficiencies of sensors and other factors. In addition, only the reflection of the sensor's signal or of the sunlight on the earth's surface is being measured, and no direct measurements are made. Consequently, the quality of maps produced by remote sensing needs to be assessed.