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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Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose
Hooft, Justin J.J. van der; Alghefari, Wejdan ; Watson, Eleanor ; Everest, Paul ; Morton, Fraser R. ; Burgess, Karl E.V. ; Smith, David G.E. - \ 2018
Metabolomics 14 (2018)11. - ISSN 1573-3882
Campylobacter jejuni - HILIC chromatography - Mass spectrometry fragmentation - Metabolomics - Sulphur metabolism

Introduction: Campylobacter jejuni is the leading cause of foodborne bacterial enteritis in humans, and yet little is known in regard to how genetic diversity and metabolic capabilities among isolates affect their metabolic phenotype and pathogenicity. Objectives: For instance, the C. jejuni 11168 strain can utilize both l-fucose and l-glutamate as a carbon source, which provides the strain with a competitive advantage in some environments and in this study we set out to assess the metabolic response of C. jejuni 11168 to the presence of l-fucose and l-glutamate in the growth medium. Methods: To achieve this, untargeted hydrophilic liquid chromatography coupled to mass spectrometry was used to obtain metabolite profiles of supernatant extracts obtained at three different time points up to 24 h. Results: This study identified both the depletion and the production and subsequent release of a multitude of expected and unexpected metabolites during the growth of C. jejuni 11168 under three different conditions. A large set of standards allowed identification of a number of metabolites. Further mass spectrometry fragmentation analysis allowed the additional annotation of substrate-specific metabolites. The results show that C. jejuni 11168 upon l-fucose addition indeed produces degradation products of the fucose pathway. Furthermore, methionine was faster depleted from the medium, consistent with previously-observed methionine auxotrophy. Conclusions: Moreover, a multitude of not previously annotated metabolites in C. jejuni were found to be increased specifically upon l-fucose addition. These metabolites may well play a role in the pathogenicity of this C. jejuni strain.

Occupancy strongly influences faecal microbial composition of wild lemurs
Umanets, Alexander ; Winter, Iris de; IJdema, Freek ; Ramiro-Garcia, Javier ; Hooft, Pim van; Heitkönig, Ignas M.A. ; Prins, Herbert H.T. ; Smidt, Hauke - \ 2018
FEMS Microbiology Ecology 94 (2018)3. - ISSN 0168-6496
Environment - Eulemur - Gastro-intestinal tract - Madagascar - Microbiota - Multivariate statistics

The microbiota of the mammalian gut is a complex ecosystem, the composition of which is greatly influenced by host genetics and environmental factors. In this study, we aim to investigate the influence of occupancy (a geographical area of habitation), species, age and sex on intestinal microbiota composition of the three lemur species: Eulemur fulvus, E. rubriventer and E. rufifrons. Faecal samples were collected from a total of 138 wild lemurs across Madagascar, and microbial composition was determined using next-generation sequencing of PCR-amplified 16S rRNA gene fragments. Consistent with reports from other primate species, the predominant phyla were Firmicutes (43 ± 6.4% [s.d.]) and Bacteroidetes (30.3 ± 5.3%). The microbial composition was strongly associated with occupancy in the E. fulvus population, with up to 19.9% of the total variation in microbial composition being explained by this factor. In turn, geographical differences observed in faecal microbiota of sympatric lemur species were less pronounced, as was the impact of the factors sex and age. Our findings showed that among the studied factors occupancy had the strongest influence on intestinal microbiota of congeneric lemur species. This suggests adaptation of microbiota to differences in forest composition, climate variations and correspondingly available diet in different geographical locations of Madagascar.

Data from: Genetic responsiveness of African buffalo to environmental stressors: a role for epigenetics in balancing autosomal and sex chromosome interactions?
Hooft, W.F. van; Dougherty, Eric R. ; Getz, Wayne M. ; Greyling, Barend J. ; Zwaan, B.J. ; Bastos, Armanda D.S. - \ 2018
sex-ratio distorter - sex-ratio suppressor - sex-ratio adjustment - microsatellite - deleterious allele - sexually-antagonistic allele - African buffalo - Syncerus caffer - Kruger National Park - epigenetics - epigenetic modification - Y chromosome - frequency-dependent selection - bovine tuberculosis - body condition
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distorter-suppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequency-dependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.
Anthropogenic disturbance effects remain visible in forest structure, but not in lemur abundances
Winter, Iris de; Hoek, Sebastiaan van der; Schütt, Jeroen ; Heitkönig, Ignas M.A. ; Hooft, Pim van; Gort, Gerrit ; Prins, Herbert H.T. ; Sterck, Frank - \ 2018
Biological Conservation 225 (2018). - ISSN 0006-3207 - p. 106 - 116.
Anthropogenic disturbance - Forest heterogeneity - Forest structure - Madagascar - Ranomafana

The persistence of tropical rainforests, together with their flora and fauna, is highly threatened by anthropogenic disturbances. In this study, we investigate to what extent selective logging influences the structure and composition of a tropical rainforest in Madagascar and subsequently lemur encounter rates and cluster sizes. We quantified forest structure variables and conducted transect surveys of seven sympatric diurnal lemur species in five protected forest sites with different logging histories. We found that DBH, tree height, the interquartile ranges of DBH and tree height (measure of forest heterogeneity), tree species and family richness were relatively high and tree density was relatively low in less disturbed compared to disturbed sites. Although the disturbed forests have not fully recovered to previous conditions, they seem to have recovered from a functional perspective into suitable lemur habitat, as lemur encounter rates and cluster sizes were similar in disturbed and less disturbed sites. We only found slightly higher encounter rates for Varecia variegata (P = 0.078) and lower encounter rates for Eulemur rufifrons (P = 0.059) in less disturbed forests. This is one of the first studies that report the presence of V. variegata, a species characterised by its drastic decline, in previously logged sites. Lemurs travelling between disturbed and less disturbed sites disperse seeds and hereby facilitate forest regeneration. Therefore, we promote the need for better attention to the value of logged forests for biodiversity conservation in Madagascar and suggest that there is considerable potential for regenerating logged forests to support lemur communities.

Lemurs on a sinking raft? : The ballast of anthropogenic disturbances
Winter, Iris I. de - \ 2018
University. Promotor(en): Herbert Prins, co-promotor(en): Ignas Heitkonig; Pim van Hooft. - Wageningen : Wageningen University - ISBN 9789463432887 - 265
Propagating annotations of molecular networks using in silico fragmentation
Silva, Ricardo R. da; Wang, Mingxun ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Fox, Evan ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Lopes, Norberto Peporine ; Dorrestein, Pieter C. - \ 2018
PLoS Computational Biology 14 (2018)4. - ISSN 1553-734X

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa
Hooft, Pim van; Keet, Dewald F. ; Brebner, Diana K. ; Bastos, Armanda D.S. - \ 2018
BMC Genetics 19 (2018)1. - ISSN 1471-2156
Disease spread - Dispersal - Gene flow - Kruger National Park - Lion - Management - Microsatellite - Mitochondrial DNA - Panthera leo - RS-3
Background: Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National Park, a bush-like ecosystem in South Africa where bovine tuberculosis prevalence ranges from low to high across a north-south gradient. Results: A total of 109 individuals sampled from 1998 to 2004 were typed using 11 microsatellite markers, and mitochondrial RS-3 gene sequences were generated for 28 of these individuals. Considerable north-south genetic differentiation was observed in both datasets. Dispersal was male-biased and generally further than 25 km, with long-distance male gene flow (75-200 km, detected for two individuals) confirming that male lions can travel large distances, even in bush-like ecosystems. In contrast, females generally did not disperse further than 20 km, with two distinctive RS-3 gene clusters for northern and southern females indicating no or rare long-distance female dispersal. However, dispersal rate for the predominantly non-territorial females from southern Kruger (fraction dispersers ≥0.68) was higher than previously reported. Of relevance was the below-average body condition of dispersers and their low presence in prides, suggesting low fitness. Conclusions: Large genetic differences between the two sampling localities, and low relatedness among males and high dispersal rates among females in the south, suggestive of unstable territory structure and high pride turnover, have potential implications for spread of diseases and the management of the Kruger lion population.
Towards Adaptive Grids for Atmospheric Boundary-Layer Simulations
Hooft, J.A. van; Popinet, Stéphane ; Heerwaarden, Chiel C. van; Linden, Steven J.A. van der; Roode, Stephan R. de; Wiel, Bas J.H. van de - \ 2018
Boundary-Layer Meteorology 167 (2018)3. - ISSN 0006-8314 - p. 421 - 443.
Adaptive mesh refinement - Atmospheric boundary layer - Direct numerical simulations - Large-eddy simulations - Turbulence
We present a proof-of-concept for the adaptive mesh refinement method applied to atmospheric boundary-layer simulations. Such a method may form an attractive alternative to static grids for studies on atmospheric flows that have a high degree of scale separation in space and/or time. Examples include the diurnal cycle and a convective boundary layer capped by a strong inversion. For such cases, large-eddy simulations using regular grids often have to rely on a subgrid-scale closure for the most challenging regions in the spatial and/or temporal domain. Here we analyze a flow configuration that describes the growth and subsequent decay of a convective boundary layer using direct numerical simulation (DNS). We validate the obtained results and benchmark the performance of the adaptive solver against two runs using fixed regular grids. It appears that the adaptive-mesh algorithm is able to coarsen and refine the grid dynamically whilst maintaining an accurate solution. In particular, during the initial growth of the convective boundary layer a high resolution is required compared to the subsequent stage of decaying turbulence. More specifically, the number of grid cells varies by two orders of magnitude over the course of the simulation. For this specific DNS case, the adaptive solver was not yet more efficient than the more traditional solver that is dedicated to these types of flows. However, the overall analysis shows that the method has a clear potential for numerical investigations of the most challenging atmospheric cases.
Genetic responsiveness of African buffalo to environmental stressors : A role for epigenetics in balancing autosomal and sex chromosome interactions?
Hooft, Pim van; Dougherty, Eric R. ; Getz, Wayne M. ; Greyling, Barend J. ; Zwaan, Bas J. ; Bastos, Armanda D.S. - \ 2018
PLoS One 13 (2018)2. - ISSN 1932-6203
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distorter-suppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequency-dependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.
A Phylogenomic Perspective on the Evolutionary History of the True Geese
Ottenburghs, J. ; Megens, H.J.W.C. ; Kraus, R.H.S. ; Hooft, W.F. van; Wieren, S.E. van; Crooijmans, R.P.M.A. ; Ydenberg, R.C. ; Groenen, M. ; Prins, H.H.T. - \ 2017
PRJEB20373 - goose phylogenomics - ERP022520
The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, contentious, the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing all seventeen species of which three subspecies of the Brent Goose, Branta bernicla) to unravel the evolutionary history of this bird group and to quantify the effects of interspecific gene flow.
Avian introgression in the genomic era
Ottenburghs, Jente ; Kraus, Robert H.S. ; Hooft, Pim van; Wieren, Sipke E. van; Ydenberg, Ronald C. ; Prins, Herbert H.T. - \ 2017
Avian Research 8 (2017)1.
Admixture - Cline theory - D-statictic - Genomic landscape - Hybridization - Phylogenetic discordance
Introgression, the incorporation of genetic material from one (sub)species into the gene pool of another by means of hybridization and backcrossing, is a common phenomenon in birds and can provide important insights into the speciation process. In the last decade, the toolkit for studying introgression has expanded together with the development of molecular markers. In this review, we explore how genomic data, the most recent step in this methodological progress, impacts different aspects in the study of avian introgression. First, the detection of hybrids and backcrosses has improved dramatically. The most widely used software package is STRUCTURE. Phylogenetic discordance (i.e. different loci resulting in discordant gene trees) is another means for the detection of introgression, although it should be regarded as a starting point for further analyses, not as a definitive proof of introgression. Specifically, disentangling introgression from other biological processes, such as incomplete lineage sorting, remains a challenging endeavour, although new techniques, such as the D-statistic, are being developed. In addition, phylogenetics might require a shift from trees to networks. Second, the study of hybrid zones by means of geographical or genomic cline analysis has led to important insights into the complex interplay between hybridization and speciation. However, because each hybrid zone study is just a single snapshot of a complex and continuously changing interaction, hybrid zones should be studied across different temporal and/or spatial scales. A third powerful tool is the genome scan. The debate on which evolutionary processes underlie the genomic landscape is still ongoing, as is the question whether loci involved in reproductive isolation cluster together in 'islands of speciation' or whether they are scattered throughout the genome. Exploring genomic landscapes across the avian tree of life will be an exciting field for further research. Finally, the findings from these different methods should be incorporated into specific speciation scenarios, which can consequently be tested using a modelling approach. All in all, this genomic perspective on avian hybridization and speciation will further our understanding in evolution in general.
A history of hybrids? Genomic patterns of introgression in the True Geese
Ottenburghs, Jente ; Megens, Hendrik Jan ; Kraus, Robert H.S. ; Hooft, Pim van; Wieren, Sipke E. van; Crooijmans, Richard P.M.A. ; Ydenberg, Ronald C. ; Groenen, Martien A.M. ; Prins, Herbert H.T. - \ 2017
BMC Evolutionary Biology 17 (2017)1. - ISSN 1471-2148
D-statistic - Hybridization - Phylogenetic Networks - Phylogenomics - PSMC
Background: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results: We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions: Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups.
Regime transitions in near-surface temperature inversions : A conceptual model
Wiel, Bas J.H. Van de; Vignon, Etienne ; Baas, Peter ; Hooijdonk, Ivo G.S. van; Linden, Steven J.A. van der; Hooft, J.A. van; Bosveld, Fred C. ; Roode, Stefan R. de; Moene, Arnold F. ; Genthon, Christophe - \ 2017
Journal of the Atmospheric Sciences 74 (2017)4. - ISSN 0022-4928 - p. 1057 - 1073.
Boundary layer - Inversions - Nonlinear models - Snow - Surface observations - Thermodynamics

A conceptual model is used in combination with observational analysis to understand regime transitions of near-surface temperature inversions at night as well as in Arctic conditions. The model combines a surface energy budget with a bulk parameterization for turbulent heat transport. Energy fluxes or feedbacks due to soil and radiative heat transfer are accounted for by a "lumped parameter closure," which represents the "coupling strength" of the system. Observations from Cabauw, Netherlands, and Dome C, Antarctica, are analyzed. As expected, inversions are weak for strong winds, whereas large inversions are found under weak-wind conditions. However, a sharp transition is found between those regimes, as it occurs within a narrow wind range. This results in a typical S-shaped dependency. The conceptual model explains why this characteristic must be a robust feature. Differences between the Cabauw and Dome C cases are explained from differences in coupling strength (being weaker in the Antarctic). For comparison, a realistic column model is run. As findings are similar to the simple model and the observational analysis, it suggests generality of the results. Theoretical analysis reveals that, in the transition zone near the critical wind speed, the response time of the system to perturbations becomes large. As resilience to perturbations becomes weaker, it may explain why, within this wind regime, an increase of scatter is found. Finally, the so-called heat flux duality paradox is analyzed. It is explained why numerical simulations with prescribed surface fluxes show a dynamical response different from more realistic surface-coupled systems.

Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes
Henquet, M.G.L. ; Prota, N. ; Hooft, J.J.J. van der; Varbanova, M. ; Hulzink, R.J.M. ; Vos, M. de; Prins, M. ; Both, M.T.J. de; Franssen, M.C.R. ; Bouwmeester, H.J. ; Jongsma, M.A. - \ 2017
The Plant Journal 90 (2017)6. - ISSN 0960-7412 - p. 1052 - 1063.
The sesquiterpenoid polygodial, belonging to the drimane family, has been shown to be an antifeedant for a number of herbivorous insects. It is presumed to be synthesized from farnesyl diphosphate via drimenol, subsequent C-12 hydroxylation, and further oxidations at both C-11 and C-12 to form a dialdehyde. Here, we have identified a drimenol synthase (PhDS) and a cytochrome P450 drimenol oxidase (PhDOX1) from Persicaria hydropiper. Expression of PhDS in yeast and plants resulted in production of drimenol only. Co-expression of PhDS with PhDOX1 in yeast yielded drimendiol, the 12-hydroxylation product of drimenol, as a major product, and cinnamolide. When PhDS and PhDOX1 were transiently expressed by agro-infiltration in Nicotiana benthamiana leaves, drimenol was almost completely converted into cinnamolide and several additional drimenol derivatives were observed. In vitro assays showed that PhDOX1 only catalyzes the conversion from drimenol to drimendiol, and not the further oxidation into an aldehyde. In yeast and heterologous plant hosts, the C-12 position of drimendiol is therefore likely further oxidized by endogenous enzymes into an aldehyde and subsequently converted to cinnamolide, presumably by spontaneous hemiacetal formation with the C-11 hydroxyl group followed by oxidation. Purified cinnamolide was confirmed by NMR and shown to be deterrent with an effective deterrent dose (ED50 ) of ~200-400 μg gFW-1 against both whiteflies and aphids. The putative additional physiological and biochemical requirements for polygodial biosynthesis and stable storage in plant tissues are discussed
Feral goats shape the Caribbean drylands
Holmgren, M. ; Coolen, Quirijn ; Debrot, A.O. ; Geurts, Kevin ; Metselaar, K. ; Oosterhuis, Henk-Jan ; Ende, Barry van den; Grinsven, Nikkie van; Hooft, W.F. van; Vergeer, Ascha - \ 2016
- 1 p.
Strong top-down goat effects on the semiarid Island of Bonaire
Grinsven, Nikkie van; Coolen, Quirijn ; Debrot, A.O. ; Geurts, Kevin ; Holmgren, M. ; Ende, Barry van den; Hooft, W.F. van - \ 2016
- 1 p.
Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
Smitz, Nathalie ; Hooft, W.F. van; Heller, Rasmus ; Cornélis, Daniel ; Chardonnet, Philippe ; Kraus, Robert ; Greyling, Ben ; Crooijmans, R.P.M.A. ; Michaux, Johan - \ 2016
population genomics - conservation - disease ecology - molecular markers - Syncerus caffer
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
Smitz, Nathalie ; Hooft, Pim van; Heller, Rasmus ; Cornélis, Daniel ; Chardonnet, Philippe ; Kraus, Robert ; Greyling, Ben ; Crooijmans, Richard ; Groenen, Martien ; Michaux, Johan - \ 2016
Mammalian Biology - Zeitschrift für Säugetierkunde 81 (2016)6. - ISSN 1616-5047 - p. 595 - 603.
Conservation - Disease ecology - Molecular markers - Population genomics

This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.

Birds in a bush : Toward an avian phylogenetic network
Ottenburghs, Jente ; Hooft, Pim van; Wieren, Sipke E. van; Ydenberg, Ronald C. ; Prins, Herbert H.T. - \ 2016
The Auk : a quarterly journal of ornithology 133 (2016)4. - ISSN 0004-8038 - p. 577 - 582.
adaptive radiation - genomics - hybridization - phylogenetic networks - Phylogenetics

Reconstructing the avian tree of life has become one of the major goals in ornithology. The use of genomic tools seemed a promising approach to reach this goal, but, instead, phylogenetic analyses of large numbers of genes uncovered high levels of incongruence between the resulting gene trees. This incongruence can be caused by several biological processes, such as recombination, hybridization, and rapid speciation (which can lead to incomplete lineage sorting). These processes directly or indirectly amount to deviations from tree-like patterns, thereby thwarting the use of phylogenetic trees. Phylogenetic networks provide an ideal tool to deal with these difficulties. We illustrate the usefulness of phylogenetic networks to capture the complexity and subtleties of diversification processes by discussing several recent genomic analyses of birds in general and the well-known radiation of Darwin's finches. With the increasing amount of genomic data in avian phylogenetic studies, capturing the evolutionary history of a set of taxa in a phylogenetic tree will become increasingly difficult. Moreover, given the widespread occurrence of hybridization and the numerous adaptive radiations in birds, phylogenetic networks provide a powerful tool to display and analyse the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

Associations between company at dinner and daily diet quality in Dutch men and women from the NQplus study
Lee, L. van; Geelen, M.M.E.E. ; Hooft Van Huysduynen, E.J.C. ; Vries, J.H.M. de; Veer, P. van 't; Feskens, E.J.M. - \ 2016
European Journal of Clinical Nutrition 70 (2016)12. - ISSN 0954-3007 - p. 1368 - 1373.
BACKGROUND/OBJECTIVES: Consuming the evening meal in the company of others has been associated with overall diet quality. Nevertheless, studies on the association between type of company at dinner and diet quality in adults are scarce.
SUBJECTS/METHODS: Dutch men (n = 895) and women (n = 845) aged between 20 and 70 years, included in a population-based observational study, were studied. Dietary intake was assessed by multiple 24-h recalls (6013 recalls) to estimate the Dutch Healthy Diet index (0–80 points) representing daily diet quality. Sex-specific linear mixed models adjusting for covariates were calculated. Out-of-home dinners and company at dinner were strongly associated (r = 0.66), and hence in additional analyses, out-of-home dinners were excluded to avoid multicollinearity.
RESULTS: Among men, daily diet quality was similar when dinners were consumed in company or consumed alone, but higher when dinner was accompanied by family (mean 46.0, s.e. 0.3) than when dinner was accompanied by others (mean 42.3, s.e. 0.7; P = 0.001). Adjustment for dinner location attenuated this association, but it remained significant when excluding out-of-home dinners. Among women, daily diet quality was lower when dinner was consumed in company (mean 48.9, s.e. 0.3) than when consumed alone (mean 51.1, s.e. 0.6; Po0.001). Dinners consumed in the company of family were associated with higher daily diet quality (mean 49.3, s.e. 0.4) than dinners consumed with others (mean 45.7, s.e. 0.6; P = 0.001). These associations persisted when excluding out-of-home dinners.
CONCLUSIONS: Only among women, dinners consumed alone as compared with dinners in company were associated with higher diet quality. In both men and women, dinners consumed with family were associated with higher diet quality as compared with dinners with others.
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