Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Selective Survival of Embryos Can Explain DNA Methylation Signatures of Adverse Prenatal Environments
Tobi, Elmar W. ; Heuvel, Joost van den; Zwaan, Bas J. ; Lumey, L.H. ; Heijmans, Bastiaan T. ; Uller, Tobias - \ 2018
Cell Reports 25 (2018)10. - ISSN 2211-1247 - p. 2660 - 2667.e4.
developmental origins - DNA methylation - plasticity - selection

An adverse intrauterine environment is associated with long-term physiological changes in offspring. These are believed to be mediated by epigenomic marks, including DNA methylation (DNAm). Changes in DNAm are often interpreted as damage or plastic responses of the embryo. Here, we propose that stochastic DNAm variation, generated during remodeling of the epigenome after fertilization, contributes to DNAm signatures of prenatal adversity through differential survival of embryos. Using a mathematical model of re-methylation in the early embryo, we demonstrate that selection, but not plasticity, will generate a characteristic reduction in DNAm variance at loci that contribute to survival. Such a reduction in DNAm variance was apparent in a human cohort prenatally exposed to the Dutch famine, illustrating that it is possible to detect a signature of selection on epigenomic variation. Selection should be considered as a possible mechanism linking prenatal adversity to subsequent health and may have implications when evaluating interventions.

Deleterious alleles in the context of domestication, inbreeding, and selection
Bosse, Mirte ; Megens, Hendrik-Jan ; Derks, Martijn F.L. ; Cara, Ángeles M.R. de; Groenen, Martien A.M. - \ 2018
Evolutionary Applications (2018). - ISSN 1752-4563
deleterious alleles - domestication - genetic load - inbreeding - selection

Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs
Yang, Bin ; Cui, Leilei ; Pérez-Enciso, M. ; Traspov, Aleksei ; Crooijmans, R.P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, M. ; Huang, L. ; Megens, H.J.W.C. - \ 2017
pig - domestication - genome - selection
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
Varroa Sensitive Hygiene contributes to naturally selected varroa resistance in honey bees
Panziera, Delphine ; Langevelde, Frank van; Blacquière, Tjeerd - \ 2017
Journal of Apicultural Research 56 (2017)5. - ISSN 0021-8839 - p. 635 - 642.
mites - resistance - selection - varroosis - VSH

The parasitic mite Varroa destructor is a serious threat for western honey bee colonies and beekeepers are compelled to control it to keep their colonies healthy. Yet, by controlling varroa no resistance to the parasite can evolve. As a trial, honey bee colonies have been left untreated in isolated locations to allow development of resistance or tolerance to the mite. These colonies developed an ability to live without control measures against varroa, although the traits responsible for this resistance or tolerance are still unclear. Two of these resistant populations have been studied to test the involvement of specific varroa mite targeted hygienic behaviour varroa sensitive hygiene (VSH) in the acquired resistance. Individual mites were manually introduced into just capped brood cells, after which the brood combs were placed in colonies of the two resistant populations and in control colonies in which varroa had always been controlled. We followed the development of the mites, including possible removals. We found that VSH had increased strongly in one of the selections, up to 40% of the infested cells with mites and pupae were removed, but it had decreased in the other selection, compared to the control colonies. Further we could not conclude from our data that VSH only or preferentially targets reproducing mites, leaving non-reproducing mites undisturbed. The different VSH responses between the two selected resistant honey bee populations lead to conclude that more than one mechanism of resistance may evolve in response to the selection pressure by varroa mites.

Selection for pure- and crossbred performance in Charolais
Vallée-Dassonneville, Amélie - \ 2017
University. Promotor(en): Johan van Arendonk; Henk Bovenhuis. - Wageningen : Wageningen University - ISBN 9789463430180 - 151
charolais - cattle - animal breeding - crossbreeding - crossbreds - selection - beef cattle - genomes - genetic parameters - rundvee - dierveredeling - kruisingsfokkerij - kruising - selectie - vleesvee - genomen - genetische parameters

Two categories of beef production exist; i.e. (i) purebred animals from a beef sire and a beef dam and (ii) crossbred animals from a beef sire and a dairy dam.

For the purebred beef production, there is a growing interest to include behavior and type traits in the breeding goal. Heritabilities for behavior traits, estimated using subjective data scored by farmers, range from 0.02 to 0.19. Heritabilities for type traits range from 0.02 to 0.35. Results show that there are good opportunities to implement selection for behavior traits using a simple on-farm recording system to allow collection of large data set, and for type traits in Charolais. A genome-wide association study detected 16 genomic regions with small effect on behavior and type traits. This suggests that behavior and type traits are influenced by many genes each explaining a small part of the genetic variance.

The two main dairy breeds mated to Charolais sires for crossbred beef production in France are Montbéliard and Holstein. The genetic correlation between the same trait measured on Montbéliard x Charolais and on Holstein x Charolais was 0.99 for muscular development, 0.96 for birth weight; and 0.91 for calving difficulty, 0.80 for height, and 0.70 for bone thinness. Thus, for these last three traits, results show evidence for re-ranking of Charolais sires depending on whether they are mated to Montbéliard or Holstein cows. When using genomic prediction, the Montbéliard x Charolais and Holstein x Charolais populations could be combined into a single reference population to increase size and accuracy of genomic prediction. Results indicate that the higher the genetic correlation is between the two crossbred populations, the higher the gain in accuracy is achieved when combining the two populations into a single reference.

The selection of Charolais sires to produce purebred or crossbred animals is made through distinct breeding programs. An alternative could be to combine selection into one breeding program. Decision for combining or keeping breeding programs separate is determined by the correlation between the breeding objectives, the selection intensity, the difference in level of genetic merit, the accuracy of selection, and the recent implementation of genomic evaluation. Considering all parameters and based on estimations for selection on birth weight, I recommend combining both breeding programs because this will lead to higher genetic gain, and might simplify operating organization and reduce associated costs.

Resistentieveredeling - Veredeling gericht op resistentie : Kennisclip Bogo-project e-learning
Hop, M.E.C.M. ; Looman, B.H.M. - \ 2016
Groen Kennisnet
resistance breeding - plant breeding - selection - selection methods - breeding programmes - breeding methods - plant protection - genetic resistance - teaching materials - resistentieveredeling - plantenveredeling - selectie - selectiemethoden - veredelingsprogramma - veredelingsmethoden - gewasbescherming - genetisch bepaalde resistentie - lesmaterialen
Deze kennisclip maakt onderdeel uit van de lesmodule Resistentie Veredeling van het CIV T&U.
Eggshell colour and disease resistance may be linked
Berghof, Tom - \ 2015
fowls - disease resistance - selection

Selection for ‘natural antibodies’ might have an effect on eggshell colour, researchers say.

Researchers at Wageningen University have found that selection for ‘natural antibodies’, a recently discovered immune characteristic, is a potential strategy to improve general disease resistance in laying hens. Selection for this immune characteristic has minimal negative consequences on production they say, but might have an effect on eggshell colour. Their findings are published in PLoS ONE and Poultry Science.

Selectie en genetische variatie in een fokprogramma
Oldenbroek, Kor ; Maurice - Van Eijndhoven, Myrthe - \ 2015
Zeldzaam huisdier 40 (2015)4. - ISSN 0929-905X - p. 14 - 17.
dierveredeling - veredelingsprogramma's - genetische variatie - selectie - zeldzame rassen - heritability - inteelt - verwantschap - groninger paard - animal breeding - breeding programmes - genetic variation - selection - rare breeds - inbreeding - kinship - groningen horse
In drie voorgaande artikelen in deze serie zijn achtereenvolgens het fokdoel, de registratie van gegevens en de basisprincipes van de erfelijkheid besproken. In dit laatste artikel wordt het belang van genetische variatie en de selectie van ouderdieren besproken. Twee belangrijke elementen in het fokprogramma van een zeldzaam ras.
Fokkerij nieuwe strategie zonder quotum
Veerkamp, Roel - \ 2015
animal breeding - cattle - breeding aims - animal breeding methods - selection - mating - animal genetics
Novel introner-like elements in fungi are involved in parallel gains of spliceosomal introns
Collemare, J. ; Beenen, H.G. ; Crous, P.W. ; Wit, P.J.G.M. de; Burgt, A. van der - \ 2015
PLoS One 10 (2015)6. - ISSN 1932-6203 - 12 p.
daphnia populations - maximum-likelihood - evolution - gene - positions - conservation - selection - sequence - genomes
Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom.
Evolution of plant growth and defense in a continental introduction
Agrawal, A.A. ; Hastings, A.P. ; Bradburst, G.S. ; Woods, E.C. ; Züst, T. ; Harvey, J.A. ; Bukovinszky, T. - \ 2015
American Naturalist 186 (2015)1. - ISSN 0003-0147 - p. E1 - E15.
milkweed asclepias-syriaca - loosestrife lythrum-salicaria - common milkweed - invasive populations - competitive ability - insect herbivores - chemical defenses - differentiation - specialist - selection
Substantial research has addressed adaptation of nonnative biota to novel environments, yet surprisingly little work has integrated population genetic structure and the mechanisms underlying phenotypic differentiation in ecologically important traits. We report on studies of the common milkweed Asclepias syriaca, which was introduced from North America to Europe over the past 400 years and which lacks most of its specialized herbivores in the introduced range. Using 10 populations from each continent grown in a common environment, we identified several growth and defense traits that have diverged, despite low neutral genetic differentiation between continents. We next developed a Bayesian modeling approach to account for relationships between molecular and phenotypic differences, confirming that continental trait differentiation was greater than expected from neutral genetic differentiation. We found evidence that growth-related traits adaptively diverged within and between continents. Inducible defenses triggered by monarch butterfly herbivory were substantially reduced in European populations, and this reduction in inducibility was concordant with altered phytohormonal dynamics, reduced plant growth, and a trade-off with constitutive investment. Freedom from the community of native and specialized herbivores may have favored constitutive over induced defense. Our replicated analysis of plant growth and defense, including phenotypically plastic traits, suggests adaptive evolution following a continental introduction.
Varied responses by yeast-like symbionts during virulence adaptation in a monophagous phloem-feeding insect
Ferrater, J.B. ; Naredo, A.I. ; Almazan, M.L.P. ; Jong, P.W. de; Dicke, M. ; Horgan, F.G. - \ 2015
Arthropod-Plant Interactions 9 (2015)3. - ISSN 1872-8855 - p. 215 - 224.
resistant rice varieties - nilaparvata-lugens homoptera - brown planthopper resistance - xylem ingestion - uric-acid - delphacidae - selection - populations - genes - aphid
This study examines the three-way interaction between symbionts, insect herbivores and their host plants during adaptation to resistant crop varieties. We conducted a long-term selection study (20 generations of continuous rearing) with a monophagous phloem-feeder, the brown planthopper [Nilaparvata lugens (Stål)], on several resistant rice (Oryza sativa L.) varieties. Planthopper fitness and the abundance of yeast-like symbionts (YLS) were monitored throughout the selection process. N. lugens populations collected from six regions in the Philippines adapted to the resistant varieties as noted by increasing body size and increased egg-laying. Adaptation was partially through physiological and behavioral changes apparent during feeding: Planthoppers on resistant plants had relatively high levels of xylem feeding compared with planthoppers on susceptible plants. YLS densities were highly dependent on the host rice variety. However, there were no consistent trends in YLS density during host plant switching and virulence adaptation: Compared to densities in planthoppers on the standard susceptible variety Taichung Native 1 (TN1), YLS densities were consistently higher on PTB33 (resistant), similar on IR62 (resistant) and IR65482 (moderately resistant) but lower on IR22 (susceptible). Furthermore, YLS densities often remained the same despite improved planthopper fitness over generations. Our results do not support the hypothesis that changes in YLS density mediate planthopper adaptation to resistant varieties. However, slight reductions in YLS densities toward the end of selection on TN1, IR22 and IR62 may indicate that YLS have lower functional significance where varieties and environmental conditions are constant between generations.
Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition
Bastiaans, E. ; Debets, A.J.M. ; Aanen, D.K. - \ 2015
Evolution 69 (2015)4. - ISSN 0014-3820 - p. 1091 - 1099.
vegetative incompatibility - neurospora-crassa - heterokaryon incompatibility - natural-populations - filamentous fungi - recognition - evolution - selection - genetics - cooperation
Allorecognition, the ability to distinguish “self” from “nonself” based on allelic differences at allorecognition loci, is common in all domains of life. Allorecognition restricts the opportunities for social parasitism, and is therefore crucial for the evolution of cooperation. However, the maintenance of allorecognition diversity provides a paradox. If allorecognition is costly relative to cooperation, common alleles will be favored. Thus, the cost of allorecognition may reduce the genetic variation upon which allorecognition crucially relies, a prediction now known as “Crozier's paradox.” We establish the relative costs of allorecognition, and their consequences for the short-term evolution of recognition labels theoretically predicted by Crozier. We use fusion among colonies of the fungus Neurospora crassa, regulated by highly variable allorecognition genes, as an experimental model system. We demonstrate that fusion among colonies is mutually beneficial, relative to absence of fusion upon allorecognition. This benefit is due not only to absence of mutual antagonism, which occurs upon allorecognition, but also to an increase in colony size per se. We then experimentally demonstrate that the benefit of fusion selects against allorecognition diversity, as predicted by Crozier. We discuss what maintains allorecognition diversity
Genetic analysis of within-litter variation in piglets’ birth weight using genomic or pedigree relationship matrices
Sell, E.B. ; Wang, Q. ; Mulder, H.A. ; Knol, E.F. - \ 2015
Journal of Animal Science 93 (2015)4. - ISSN 0021-8812 - p. 1471 - 1480.
generalized linear-models - single nucleotide polymorphism - environmental variance - broiler-chickens - residual variance - individual birth - breeding values - parameters - heterogeneity - selection
The objective of this study was to estimate the genetic variance for within-litter variation of birth weight (BW0) using genomic (GRM) or pedigree relationship matrices (PRM) and to compare the accuracy of estimated breeding values (EBV) for within-litter variation of BW0 using GRM and PRM. The BW0 and residual variance of BW0 were modeled by the double hierarchical generalized linear model using GRM or PRM. Data came from 2 dam lines: Landrace and Large White. After editing, the data set in Landrace consisted of 748 sows with 1,938 litters and 29,430 piglets and in Large White of 989 sows with 3,320 litters and 51,818 piglets. To construct GRM, 46,466 (Landrace) and 44,826 (Large White) single nucleotide polymorphisms were used, whereas to construct PRM, 5 generations of pedigree were used. The accuracy of EBV with GRM was estimated with 8-fold cross-validation and compared to PRM. Estimated variance components were highly similar for GRM and PRM. The maternal genetic variance in residual variance of BW0 in Landrace was 0.05 with GRM and 0.06 with PRM. In Large White these were 0.04 with GRM and 0.05 with PRM. The genetic coefficient of variation (GCVSDe) was about 0.10 in both dam lines. This indicates a change of 10% in residual SD of BW0 when achieving a genetic response of 1 genetic standard deviation. The genetic correlation between birth weight and its residual variance was about 0.6 in both dam lines. The accuracies of selection for within-litter variation of birth weight were 0.35 with GRM and 0.23 with PRM in Landrace and 0.29 with GRM and 0.34 with PRM in Large White. In this case, using GRM did not significantly increase accuracies of selection. Results, however, show good opportunities to select for reduced within-litter variation of BW0. Genomic selection can increase accuracy of selection when reference populations contain at least 2,000 sows
Heterogeneity in genetic variation and energy sink relationships for residual feed intake across research stations and countries
Tempelman, R. ; Spurlock, D.M. ; Coffey, M.P. ; Veerkamp, R.F. ; Armentano, L. ; Weigel, K. ; Haas, Y. de; Staples, C.R. ; Connor, E.E. ; Hanigan, M.D. ; Lu, Y.F. ; Haar, M.J. van de - \ 2015
Journal of Dairy Science 98 (2015)3. - ISSN 0022-0302 - p. 2013 - 2026.
random regression-models - dairy-cattle - lactation performance - efficiency - cows - selection - supplementation - heritability - components - variance
Our long-term objective is to develop breeding strategies for improving feed efficiency in dairy cattle. In this study, phenotypic data were pooled across multiple research stations to facilitate investigation of the genetic and nongenetic components of feed efficiency in Holstein cattle. Specifically, the heritability of residual feed intake (RFI) was estimated and heterogeneous relationships between RFI and traits relating to energy utilization were characterized across research stations. Milk, fat, protein, and lactose production converted to megacalories (milk energy; MilkE), dry matter intakes (DMI), and body weights (BW) were collected on 6,824 lactations from 4,893 Holstein cows from research stations in Scotland, the Netherlands, and the United States. Weekly DMI, recorded between 50 to 200 d in milk, was fitted as a linear function of MilkE, BW0.75, and change in BW (¿BW), along with parity, a fifth-order polynomial on days in milk (DIM), and the interaction between this polynomial and parity in a first-stage model. The residuals from this analysis were considered to be a phenotypic measure of RFI. Estimated partial regression coefficients of DMI on MilkE and on BW0.75 ranged from 0.29 to 0.47 kg/Mcal for MilkE across research stations, whereas estimated partial regression coefficients on BW0.75 ranged from 0.06 to 0.16 kg/kg0.75. Estimated partial regression coefficients on ¿BW ranged from 0.06 to 0.39 across stations. Heritabilities for country-specific RFI were based on fitting second-stage random regression models and ranged from 0.06 to 0.24 depending on DIM. The overall heritability estimate across all research stations and all DIM was 0.15±0.02, whereas an alternative analysis based on combining the first- and second-stage model as 1 model led to an overall heritability estimate of 0.18±0.02. Hence future genomic selection programs on feed efficiency appear to be promising; nevertheless, care should be taken to allow for potentially heterogeneous variance components and partial relationships between DMI and other energy sink traits across environments when determining RFI.
Impact of QTL properties on the accuracy of multi-breed genomic prediction
Wientjes, Y.C.J. ; Calus, M.P.L. ; Goddard, M.E. ; Hayes, B.J. - \ 2015
Genetics, Selection, Evolution 47 (2015). - ISSN 0999-193X
dairy-cattle populations - residual feed-intake - complex traits - linkage disequilibrium - genotype imputation - data sets - selection - values - animals - reliability
Background - Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows. Methods - Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect. Results - For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects. Conclusions - Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.
Deriving animal behaviour from high-frequency GPS: tracking cows in open and forested habitat
Weerd, N. de; Langevelde, F. van; Oeveren, H. van; Nolet, B.A. ; Kölzsch, A. ; Prins, H.H.T. ; Boer, W.F. de - \ 2015
PLoS One 10 (2015)6. - ISSN 1932-6203 - 17 p.
collar performance - large herbivores - telemetry data - movement - cattle - ecology - states - technology - selection - position
The increasing spatiotemporal accuracy of Global Navigation Satellite Systems (GNSS) tracking systems opens the possibility to infer animal behaviour from tracking data.We studied the relationship between high-frequency GNSS data and behaviour, aimed at developing an easily interpretable classification method to infer behaviour from location data. Behavioural observations were carried out during tracking of cows (Bos Taurus) fitted with high-frequency GPS (Global Positioning System) receivers. Data were obtained in an open field and forested area, and movement metrics were calculated for 1 min, 12 s and 2 s intervals. We observed four behaviour types (Foraging, Lying, Standing and Walking). We subsequently used Classification and Regression Trees to classify the simultaneously obtained GPS data as these behaviour types, based on distances and turning angles between fixes. GPS data with a 1 min interval from the open field was classified correctly for more than 70% of the samples. Data from the 12 s and 2 s interval could not be classified successfully, emphasizing that the interval should be long enough for the behaviour to be defined by its characteristic movement metrics. Data obtained in the forested area were classified with a lower accuracy (57%) than the data from the open field, due to a larger positional error of GPS locations and differences in behavioural performance influenced by the habitat type. This demonstrates the importance of understanding the relationship between behaviour and movement metrics, derived from GNSS fixes at different frequencies and in different habitats, in order to successfully infer behaviour. When spatially accurate location data can be obtained, behaviour can be inferred from high-frequency GNSS fixes by calculating simple movement metrics and using easily interpretable decision trees. This allows for the combined study of animal behaviour and habitat use based on location data, and might make it possible to detect deviations in behaviour at the individual level.
Controlling the structure and length of self-synthesizing supramolecular polymers through nucleated growth and disassembly
Pal, A. ; Malakoutikhah, M. ; Leonetti, G. ; Tezcan, M. ; Colomb-Delsuc, M. ; Nguyen, V.D. ; Gucht, J. van der; Otto, S. - \ 2015
Angewandte Chemie-International Edition 54 (2015)27. - ISSN 1433-7851 - p. 7852 - 7856.
dynamic combinatorial libraries - systems chemistry - co-micelles - polymerization - replication - driven - complexity - mechanism - selection
Directing self-assembly processes out-of-equilibrium to yield kinetically trapped materials with well-defined dimensions remains a considerable challenge. Kinetically controlled assembly of self-synthesizing peptide-functionalized macrocycles through a nucleation–growth mechanism is reported. Spontaneous fiber formation in this system is effectively shut down as most of the material is diverted into metastable non-assembling trimeric and tetrameric macrocycles. However, upon adding seeds to this mixture, well-defined fibers with controllable lengths and narrow polydispersities are obtained. This seeded growth strategy also allows access to supramolecular triblock copolymers. The resulting noncovalent assemblies can be further stabilized through covalent capture. Taken together, these results show that self-synthesizing materials, through their interplay between dynamic covalent bonds and noncovalent interactions, are uniquely suited for out-of-equilibrium self-assembly.
Individual-area relationship best explains goose species density in wetlands
Zhang, Y. ; Jia, Q. ; Prins, H.H.T. ; Cao, L. ; Boer, W.F. de - \ 2015
PLoS One 10 (2015)5. - ISSN 1932-6203 - 11 p.
human disturbance - habitat heterogeneity - mammalian herbivores - population-density - african elephant - forage quality - barnacle geese - body-mass - diversity - selection
Explaining and predicting animal distributions is one of the fundamental objectives in ecology and conservation biology. Animal habitat selection can be regulated by top-down and bottom-up processes, and is mediated by species interactions. Species varying in body size respond differently to top-down and bottom-up determinants, and hence understanding these allometric responses to those determinants is important for conservation. In this study, using two differently sized goose species wintering in the Yangtze floodplain, we tested the predictions derived from three different hypotheses (individual-area relationship, food resource and disturbance hypothesis) to explain the spatial and temporal variation in densities of two goose species. Using Generalized Linear Mixed Models with a Markov Chain Monte Carlo technique, we demonstrated that goose density was positive correlated with patch area size, suggesting that the individual area-relationship best predicts differences in goose densities. Moreover, the other predictions, related to food availability and disturbance, were not significant. Buffalo grazing probably facilitated greater white-fronted geese, as the number of buffalos was positively correlated to the density of this species. We concluded that patch area size is the most important factor determining the density of goose species in our study area. Patch area size is directly determined by water levels in the Yangtze floodplain, and hence modifying the hydrological regimes can enlarge the capacity of these wetlands for migratory birds.
Fitness consequences of indirect plant defence in the annual weed, Sinapis arvensis
Gols, R. ; Wagenaar, R. ; Poelman, E.H. ; Kruidhof, H.M. ; Loon, J.J.A. van; Harvey, J.A. - \ 2015
Functional Ecology 29 (2015)8. - ISSN 0269-8463 - p. 1019 - 1025.
pieris-brassicae - herbivory - tolerance - evolution - volatiles - insects - parasitoids - strategies - selection - ecology
Plant traits that enhance the attraction of the natural enemies of their herbivores have been postulated to function as an 'indirect defence'. An important underlying assumption is that this enhanced attraction results in increased plant fitness due to reduced herbivory. This assumption has been rarely tested. We investigated whether there are fitness consequences for the charlock mustard Sinapis arvensis, a short-lived outcrossing annual weedy plant, when exposed to groups of large cabbage white (Pieris brassicae) caterpillars parasitized by either one of two wasp species, Hyposoter ebeninus and Cotesia glomerata, that allow the host to grow during parasitism. Hyposoter ebeninus is solitary and greatly reduces host growth compared with healthy caterpillars, whereas C. glomerata is gregarious and allows the host to grow approximately as large as unparasitized caterpillars. Both healthy and parasitized P. brassicae caterpillars initially feed on the foliage, but later stages preferentially consume the flowers. In a garden experiment, plants damaged by parasitized caterpillars produced more seeds than conspecific plants damaged by unparasitized caterpillars. Reproductive potential (germination success multiplied by total seed number) was similar for plants that were not exposed to herbivory and those that were damaged by parasitized caterpillars and lower for plants that were damaged by healthy unparasitized caterpillars. However, these quantitative seed traits negatively correlated with the qualitative seed traits, individual seed size and germination success, suggesting a trade-off between these two types of traits. We show that parasitism of insect herbivores that feed on reproductive plant tissues may have positive fitness consequences for S. arvensis. The extent to which plant fitness may benefit depends on parasitoid lifestyle (solitary or gregarious), which is correlated with the amount of damage inflicted on these tissues by the parasitized host
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