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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    Genetische monitoring van de Nederlandse otterpopulatie : ontwikkeling van populatieomvang en genetische status 2014/2015
    Kuiters, A.T. ; Groot, G.A. de; Lammertsma, D.R. ; Jansman, H.A.H. ; Bovenschen, J. - \ 2016
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 62) - 30
    lutra lutra - otters - populatiegenetica - inteelt - mortaliteit - monitoring - nederland - lutra lutra - otters - population genetics - inbreeding - mortality - monitoring - netherlands
    Jaarlijks wordt de Nederlandse otterpopulatie genetisch gemonitord in opdracht van het Ministerie van
    Economische Zaken. Daarmee wordt een vinger aan de pols gehouden wat betreft de ontwikkeling van de
    genetische status van de populatie. Deze vorm van monitoring, waarbij gebruik wordt gemaakt van DNA
    geïsoleerd uit uitwerpselen en doodvondsten, maakt het tevens mogelijk veranderingen in de ruimtelijke
    verspreiding en de populatieomvang te volgen. De monitoringsronde van 2014/2015 laat zien dat de
    populatie verder is gegroeid naar ca. 160 individuen. Op populatieniveau lijkt geen verder verlies aan
    genetische variatie te zijn opgetreden. De genetische variatie binnen individuen is evenmin verder
    afgenomen in tegenstelling tot voorafgaande jaren. Onderdeel van deze monitoring is ook autopsie van dode
    otters, waarbij wordt gekeken naar de doodsoorzaak en de belangrijkste lichaamskenmerken. Verkeer is
    verreweg de belangrijkste doodsoorzaak. Locaties waar otters worden doodgereden, worden geregistreerd
    en bijgehouden in een database. Deze informatie is belangrijk voor het veiliger maken van knelpuntlocaties
    om zo het aantal verkeersslachtoffers te beperken. Het aantal verkeersslachtoffers neemt nog ieder jaar toe,
    waarbij de toename evenredig is aan de toename in de populatieomvang
    Genetische monitoring van de Nederlandse otterpopulatie 2013/2014 : ontwikkeling van populatieomvang en populatiegenetische status
    Kuiters, A.T. ; Groot, G.A. de; Lammertsma, D.R. ; Jansman, H.A.H. ; Bovenschen, J. - \ 2015
    Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2624) - 39
    lutra lutra - otters - fauna - populatiedichtheid - populatiegenetica - inteelt - mortaliteit - dna - monitoring - friesland - noordwest-overijssel - drenthe - lutra lutra - otters - fauna - population density - population genetics - inbreeding - mortality - dna - monitoring - friesland - noordwest-overijssel - drenthe
    Jaarlijks wordt in opdracht van het ministerie van Economische Zaken de Nederlandse otterpopulatie genetisch gemonitord. Daarmee wordt een vinger aan de pols gehouden wat betreft de ontwikkeling van de genetische status van de populatie. Deze vorm van monitoring, gebaseerd op DNA-profielen op basis van DNA geïsoleerd uit verse spraints (uitwerpselen), maakt het tevens mogelijk veranderingen in de ruimtelijke verspreiding en de populatieomvang van jaar tot jaar te volgen. De monitoringsronde van 2013/2014 laat zien dat de populatie verder is gegroeid naar een aantal van ca. 140 individuen. Echter, de genetische variatie binnen individuen is sterker afgenomen vergeleken met voorafgaande jaren. Onderdeel van deze monitoring is ook autopsie van dode otters, waarbij wordt gekeken naar de doodsoorzaak en de belangrijkste lichaamskenmerken. Knelpuntlocaties waar otters worden doodgereden worden in beeld gebracht. Er is een sterke toename van het jaarlijkse aantal verkeersslachtoffers. Deze lijkt gelijke tred te houden met de toename van de populatieomvang.
    Population genetics and disease ecology of European wild boar
    Goedbloed, D.J. - \ 2013
    Wageningen University. Promotor(en): Herbert Prins; Ron Ydenberg, co-promotor(en): Pim van Hooft. - S.l. : s.n. - ISBN 9789461737236 - 123
    wilde varkens - sus scrofa - infectieziekten - populatiegenetica - ecologie - mycoplasma hyopneumoniae - varkenscircovirus-1 - ziekteoverdracht - fauna - noordwest-europa - wild pigs - sus scrofa - infectious diseases - population genetics - ecology - mycoplasma hyopneumoniae - porcine circovirus-1 - disease transmission - fauna - northwestern europe
    Welke factoren beïnvloeden de frequentie van de ziekten in wilde populaties? Het promotieonderzoek van Daniel Goedbloed beoordeelde de invloed van demografische, genetische en omgevingsfactoren op de frequentie van twee infectieziekten in Noordwest-Europese wilde zwijnen populaties.
    Advies voor genetisch beheer van de Bonte Bentheimen populatie in Nederland
    Windig, J.J. ; Hoving, A.H. - \ 2013
    Wageningen : Centre for genetic resources (CGN) (CGN rapport 28) - 16
    varkens - beren (varkens) - kunstmatige inseminatie - fokkerijmethoden - dierveredeling - populatiegenetica - genetische bronnen van diersoorten - varkensrassen - zeldzame rassen - pigs - boars - artificial insemination - animal breeding methods - animal breeding - population genetics - animal genetic resources - pig breeds - rare breeds
    De Bonte Bentheimer heeft in Nederland een kleine populatieomvang. In kleine rassen kan inteelt voor grote problemen zorgen en dus is een goed fokbeleid nodig om een te sterke inteelttoename te voorkomen.
    Genetica van wilde zwijnen in Limburg en Noord-Brabant : verspreiding, herkomst en verwantschap
    Jansman, H.A.H. ; Hofmeester, T.R. ; Groot, G.A. de; Laros, I. ; Bovenschen, J. ; Speelman, M. ; Hout, J.J. van der; Casaer, J. ; Breyne, P. ; Koelewijn, H.P. - \ 2013
    Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2404) - 62
    sus scrofa - wilde varkens - populatiedynamica - populatiegenetica - genetica - migratie - limburg - noord-brabant - fauna - sus scrofa - wild pigs - population dynamics - population genetics - genetics - migration - limburg - noord-brabant - fauna
    In Limburg komen op verschillende plaatsen buiten het officiële leefgebied De Meinweg wilde zwijnen voor. De aantallen in deze zogenaamde nulstandsgebieden nemen toe, en ook in Noord-Brabant worden in toenemende mate wilde zwijnen gesignaleerd. In opdracht van de provincies Limburg en Noord-Brabant voerde Alterra een genetisch onderzoek uit naar de populatiestructuur en herkomst van de wilde zwijnen in Limburg en Noord-Brabant. Het onderzoek laat zien dat sprake is van een aantal afzonderlijke populaties met een unieke genetische samenstelling. Door gunstigere omstandigheden weten de populaties van wilde zwijnen in Noordwest Europa in aantal en verspreidingsgebied toe te nemen. Genetisch kon dan ook vastgesteld worden dan in de meeste gevallen de nieuwe populaties ontstaan zijn uit de naburige bestaande populaties. In enkele gevallen kan sprake zijn geweest van een (gedeeltelijke) onnatuurlijke oorsprong door ontsnappingen uit gevangenschap of illegale herintroducties. De genetische variatie in de populaties is redelijk, maar laag vergeleken met het buitenland. Onder de huidige omstandigheden lijkt de uitwisseling tussen deze jonge populaties echter voldoende om de variatie in de toekomst op z'n minst in stand te houden.
    Genetische tools voor natuurbeheer: van het lab naar de praktijk
    Groot, G.A. de; Laros, I. - \ 2013
    Vakblad Natuur Bos Landschap 10 (2013)4. - ISSN 1572-7610 - p. 4 - 7.
    natuurbeheer - genetische diversiteit - populatiegenetica - populatie-ecologie - nature management - genetic diversity - population genetics - population ecology
    Genetische technieken worden nog altijd maar mondjesmaat gebruikt in het natuurbeheer en -beleid. Dit is deels het gevolg van een imagoprobleem: in het verleden waren deze technieken prijzig, en de toepassingsmogelijkheden beperkt. De moleculaire ecologie staat echter niet stil en nieuwe ontwikkelingen volgen elkaar in hoog tempo op. Gevestigde technieken hebben hun concrete waarde voor beleidsvorming en praktisch populatiebeheer inmiddels bewezen, en werden prijstechnisch steeds interessanter. Nieuwe technieken bieden een efficïënt alternatief voor conventionele inventarisaties. Tijd voor een update.
    Genetic diversity and population structure of cucumber (Cucumis sativus L.)
    Lv, J. ; Qi, J. ; Shi, Q. ; Shen, D. ; Zhang, S. ; Shao, G. ; Li, H. ; Sun, Z. ; Weng, Y. ; Shang, Y. ; Gu, X. ; Li, X. ; Zhu, X. ; Zhang, J. ; Treuren, R. van; Dooijeweert, W. van; Zhang, Z. ; Huang, S. - \ 2012
    PLoS ONE 7 (2012)10. - ISSN 1932-6203 - 9
    genetische diversiteit - cucumis sativus - komkommers - populatiegenetica - genenbanken - dna-fingerprinting - germplasm - genetische merkers - vruchtgroenten - groenten - genetic diversity - cucumis sativus - cucumbers - population genetics - gene banks - dna fingerprinting - germplasm - genetic markers - fruit vegetables - vegetables - genome - map
    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.
    The role of Mallard (Anas platyrhynchos) in the spread of avian influenza: genomics, population genetics, and flyways
    Kraus, R.H.S. - \ 2011
    Wageningen University. Promotor(en): Herbert Prins; Ron Ydenberg, co-promotor(en): Pim van Hooft. - [S.l.] : S.n. - ISBN 9789461730282 - 143
    aviaire influenzavirussen - aviaire influenza - anas platyrhynchos - ziekteoverdracht - vogeltrek - genomica - populatiegenetica - evolutionaire genetica - zoögeografie - bioveiligheid - ziekteoverzichten - epidemiologie - avian influenza viruses - avian influenza - anas platyrhynchos - disease transmission - bird migration - genomics - population genetics - evolutionary genetics - zoogeography - biosafety - disease surveys - epidemiology

    Birds, in particular poultry and ducks, are a source of many infectious diseases, such as those caused by influenza viruses. These viruses are a threat not only to the birds themselves but also to poultry farming and human health, as forms that can infect humans are known to have evolved. It is believed that migratory birds in general play an important role in the global spread of avian influenza (AI). However, it is still debated how large this role precisely is and whether other modes of spread may be more important. The mallard (Anas platyrhynchos) is the world’s most abundant and well-studied waterfowl species. Besides being an important game and agricultural species, it is also a flagship species in wetland conservation and restoration. Waterfowl (Anseriformes: Anatidae) and especially ducks currently are the focal bird group in long distance dispersal of Avian Influenza in the wild, and the mallard has been identified as the most likely species to transport this virus.

    In my thesis I report aspects of the biology of this important host species of AI by molecular ecological means. As molecular marker system I established a genome-wide set of more than 100,000 SNPs of which I developed a subset of 384 SNPs into an assay to genotype about 1,000 ducks. This subset was employed to study the evolutionary history and speciation processes in the Anas genus. Further investigations into the world-wide mallard population structure on a species level were based not only on this set of 384 SNPs but also on mitochondrial DNA sequences. Last but not last, I investigated an option of AI sampling and detection from duck faeces by technology that is safe from a biohazard perspective, and solves transportation issues related to cold chains.

    The main results of my thesis include the development of a generally applicable improved analysis pipeline to develop genome-wide SNP sets for non-model organisms. Further, my results show that, from a migration system perspective, mallard flyways/populations can hardly be delineated from a biological point of view. Detailed phylogenetic, population genetic and coalescent analyses of a data set of samples spanning the whole northern hemisphere leads me to conclude that the only firm population boundaries that I can draw are between Eurasia and North America, within which panmixia is almost achieved. Mallards’ and other Anas-ducks’ whole continental to global distribution brings them together in sympatry. I can show that a combination of sympatric distribution, conflicting genetically determined and learned mate recognition mechanisms, and genomic compatibility between species helps to explain the long-standing puzzle of waterfowl hybridisation and introgression of genes from one duck species into another. Besides obvious management implications I propose that this fact can be part of the explanation why ducks are so well adaptable and successful, as well as why they show extraordinary abilities to withstand AI infections, or its consequences for health status.

    Genetic variation in the chicken genome: insights in selection
    Elferink, M.G. - \ 2011
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Richard Crooijmans. - [S.l.] : S.n. - ISBN 9789085859208 - 162
    pluimvee - dierveredeling - genomen - populatiegenetica - genen - rassen (dieren) - genetische kartering - genetische variatie - selectie - poultry - animal breeding - genomes - population genetics - genes - breeds - genetic mapping - genetic variation - selection

    The chicken currently provides more than a quarter of the meat and nearly all eggs produced worldwide. For future improvements in production traits and animal welfare as well as to address future consumer demands it is necessary to understand the etiology and biology underlying production traits and diseases. The primary aim of the research described in this thesis was to investigate the utility of several molecular approaches to identify causative variants underlying a variety of traits in the chicken.
    The general introduction in chapter 1 provides an overview of the domestication history of the chicken - with a particular focus on commercial chicken breeds - and describes the importance to identify causative variants underlying production traits and diseases. Furthermore, several different molecular techniques and methods are introduced that are being used to detect causative variants underlying monogenic and polygenic traits.
    Linkage maps are essential for linkage analysis, important to study recombination rates and recombination hotspots within the genome and can assist in the sequence assembly of genomes. In chapter 2 we describe the construction of a new high-resolution linkage map of the chicken genome based on two chicken populations with a total of 1619 individuals. The two populations used are a purebred broiler line and a broiler x broiler cross. This high resolution allowed accurate identification of recombination hotspots in the chicken genome, including sex specific recombination. Furthermore, to improve the current reference genome (WASHUC2), 613 unmapped markers were included in the genome-wide assay that included a total of 17,790 SNPs. The resulting linkage map comprises 13,340 SNPs, of which 360 had not been assigned to a known chromosome on chicken genome build WASHUC2. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. Regional differences in recombination hotspots between the two mapping populations were observed for several chromosomes near the telomere of the p arm. The sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
    In chapter 3 we describe the molecular characterization of the locus causing the late feathering phenotype; a monogenic trait in chicken that results in a delayed emergence of flight feathers at hatch. The late feathering phenotype is beneficial to breeders as it can be used for sex typing at hatch. The locus has, therefore, been extensively used in diverse commercial chicken breeds. However, a retrovirus closely linked to the late feathering allele causes a negative pleiotropic effect on egg production and causes viral infections. Within this chapter we describe the identification of a 180 kb tandem duplication in the late feathering allele using a quantitative PCR approach. The tandem duplication results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. Sequence analysis revealed that the duplication is identical in broiler, white egg-layer, and brown egg-layer lines. This information was also used to design a molecular test to detect this duplication, particularly in heterozygous individuals.
    The recent advances in massive parallel sequencing technologies have enabled rapid and cost-effective detection of all genetic variants within genomes. The detection of all genetic variants within a genome has further increased our ability to identify causative variants underlying quantitative trait loci (QTL). In chapter 4, we combined a genome-wide association study with whole-genome resequencing to identify causative variants underlying the pulmonary hypertension syndrome (PHS), a polygenic trait in chicken. PHS is a metabolic disease that has been linked to intense selection on growth rate and feed conversion ratio of modern broilers (meat-type chicken). PHS has become one of the most frequent causes of mortality within the broiler industry and leads to substantial economic losses and reduced animal welfare. In total, 18 QTL regions were identified in the genome-wide association study. In order to detect causative variants underlying these QTL regions, we sequenced the genomes of twelve individuals. To maximize the detection of causative variants we selected the individuals based on extreme phenotypes for PHS. Within 8 QTL regions we identified a total of 10 genes that contain at least one variant that is predicted to affect protein function. Moreover, 7.62 million SNPs were detected within the twelve animals compared to the reference genome. These markers can be used in the development of future genome-wide assays.
    Genomic regions that have undergone selection should contain loci that influence important phenotypic traits and will, therefore, include causative variant(s) that could aid in further future improvement of production traits and disease resistance. In chapter 5, we applied hitch-hiking mapping to make a broad assessment of the effects of selection histories in domesticated chicken. Towards this end, we sampled commercial chickens representing all major breeding goals from multiple breeding companies. In addition, we sampled non-commercial chicken diversity by sampling almost all recognized traditional Dutch breeds and a representative sample of breeds from China. The broad sample of 67 commercial and non-commercial breeds were assessed for signatures of selection in the genome using information of 57,636 SNPs that were genotyped on pooled DNA samples. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations. The detection of regions of putative selection resulted in the identification of several candidate genes that could aid in further improvement of production traits and disease resistance.
    Finally, the general discussion in chapter 6 describes the main findings of this thesis. In this chapter recommendations are given for the best strategies to detect causative variants underlying monogenic or polygenic traits. All strategies can benefit substantially from the recent developments in massive parallel sequencing, although the high costs of this method currently prevent large scale studies. In order to perform powerful and cost-effective studies, several strategies are discussed that combine massive parallel sequencing with other existing methods and techniques. Furthermore, the limitations of the different strategies are addressed, as well as the improvements needed in the near future to identify causative variants underlying a variety of traits in, but not limited to, the chicken.



    Estimating genetic diversity across the neutral genome with the use of dense marker maps
    Engelsma, K.A. ; Calus, M.P.L. ; Bijma, P. ; Windig, J.J. - \ 2010
    Genetics, Selection, Evolution 42 (2010). - ISSN 0999-193X - 10
    populatiegenetica - computersimulatie - genetische diversiteit - merkergenen - population genetics - computer simulation - genetic diversity - marker genes - linkage disequilibrium - prediction - selection - conservation - populations - haplotypes
    Background With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity. Results The simulated population had an average minor allele frequency of 0.28 and an LD (r2) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity. Conclusions Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.
    Levels of inbreeding in group mating captive broodstock populations of Common sole, (Solea solea), inferred from parental relatedness and contribution
    Blonk, R.J.W. ; Komen, J. ; Kamstra, A. ; Crooijmans, R.P.M.A. ; Arendonk, J.A.M. van - \ 2009
    Aquaculture 289 (2009)1-2. - ISSN 0044-8486 - p. 26 - 31.
    vissen - tong (vis) - voortplanting - natuurlijke paring - populatiegenetica - nageslacht - inteelt - kuitschieten - afstamming - heterozygotie - genetische diversiteit - genetische bronnen - fishes - dover soles - reproduction - natural mating - population genetics - progeny - inbreeding - spawning - parentage - heterozygosity - genetic diversity - genetic resources - cod gadus-morhua - fish breeding programs - dover sole - spawning aggregations - scophthalmus-maximus - reproductive success - genetic-variation - mass selection - dna markers - senegalensis
    In this paper, we estimate levels of inbreeding with parental relatedness and contribution inferred from microsatellites in groups of Common sole that reproduce by natural mating. We present results on spawning patterns during one entire reproductive season of wild Common sole, Solea solea, kept in two broodstock groups (28 animals in broodstock A; 20 animals in broodstock B) under semi-natural conditions. Batches of eggs were collected daily and incubated separately. First, we performed a parentage analysis on parents and samples of 24 newly hatched larvae from all batches, using 10 polymorphic microsatellite markers. As expected, contribution of parents to offspring was highly skewed. In both broodstocks, five or less parental pairs produced more than half of the total progeny. Natural spawning and unequal contributions of parents to offspring resulted in significant deviations from Hardy–Weinberg equilibria. Furthermore, few alleles were lost and levels of heterozygosity in offspring population increased. Next, we calculated relatedness between parents that mated successfully based on estimates of molecular similarity. Mean coefficients of coancestry in offspring were determined using parental relatedness and contributions. Levels of coancestry in progeny were substantially high. These results show that due to different parental contributions, natural mating in groups can result in significant inbreeding in future generations despite of limited loss of alleles and high levels of heterozygosity in first generation progeny. This shows that using loss of alleles and levels of heterozygosity alone can be misleading for estimation of genetic diversity.
    Genetic conservation of endangered animal populations
    Oliehoek, P.A. - \ 2009
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma. - [S.l.] : S.n. - ISBN 9789085853503 - 113
    dieren - genetische diversiteit - inteelt - bedreigde soorten - bedreigde rassen - stamboom - populatiegenetica - populaties - conservering - ex-situ conservering - animals - genetic diversity - inbreeding - endangered species - endangered breeds - pedigree - population genetics - populations - conservation - ex situ conservation
    Genetic factors in metapopulation survival : introduction to a PhD-project
    Cobben, M.M.P. ; Arens, P.F.P. ; Verboom, J. ; Smulders, M.J.M. - \ 2008
    habitats - populatiegenetica - demografie - distributie - conservering - genetische diversiteit - klimaatverandering - simulatiemodellen - metapopulaties - ecologische hoofdstructuur - habitats - population genetics - demography - distribution - conservation - genetic diversity - climatic change - simulation models - metapopulations - ecological network
    Short introduction to a PhD project. Which factors determine the level and distribution of genetic diversity in fragmented populations, and how are these affected by increased temperature and weather variability? METAPHOR, a stochastic, spatially explicit, individual-based simulation model for demography of fragmented populations, will be extended with a genetic module to explore these research questions
    Effects of population size on virus evolution: a baculovirus perspective
    Zwart, M.P. - \ 2008
    Wageningen University. Promotor(en): Just Vlak, co-promotor(en): Wopke van der Werf; Arjan de Visser. - S.l. : S.n. - ISBN 9789085049920 - 140
    baculovirus - populatiegenetica - autographa californica - insectenvirussen - virusziekten - infectie - polymerase-kettingreactie - evolutie - waarschijnlijkheidsmodellen - genotypen - dna-virussen - virus-gastheer interacties - baculovirus - population genetics - autographa californica - insect viruses - viral diseases - infection - polymerase chain reaction - evolution - probabilistic models - genotypes - dna viruses - virus-host interactions
    This thesis explores the population genetics of the baculovirus infection process and the consequences for virus evolution. Using Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) and lepidopteran insect larvae as a model system, we attempt to characterize (1) elemental virus-host and virus-virus interactions pertinent to virus invasion and disease of the host, focussing largely on the number of virus individuals invading a host insect and including the first strong experimental evidence that a single virion can cause disease in a host animal, and (2) the interactions that can occur between virus genotypes during the process of diseasing the host, specifically competition.
    The development of two technologies was necessary to address these questions. First, a method for generating clonal baculovirus populations containing molecular tag sequences was devised: insect larvae were transfected with full-length baculovirus genomic DNA modified to allow replication in Escherichia coli (bacmids). Second, a quantitative real-time PCR (qPCR) based assay was developed to measure the frequency of a baculovirus genotype in a mixed population.
    In order to estimate the number of pathogen individuals invading the host and causing death, a basic probabilistic model that links this number to host survival was developed and experimentally tested. This model is based on the independent action hypothesis (IAH): the notion that (1) every pathogen individual has a fixed probability of invading the host, (2) if a pathogen individual invades the host this will irrevocably lead to host death, and (3) that pathogen individuals act independently. Here the model was specifically developed to predict how often hosts are invaded by two pathogen genotypes, when being challenged by a pathogen population consisting of two genotypes. Model predictions were tested using two near-identical bacmid-derived virus genotypes, larvae of three host species, and the qPCR assay. IAH model predictions were confirmed in early instar (L3) larvae of permissive host species (Spodoptera exigua and Trichoplusia ni). This strongly suggests that in these instances it is the action of one invading virion which leads to host death. Model predictions did not hold for late instar larvae (L5) of permissive host species and both early and late larvae of a semi-permissive species (Mamestra brassicae), which show greater resistance to AcMNPV. In these instances there was a too high frequency of invasions with both genotypes, suggesting that more virions had invaded these larvae to cause disease than predicted by IAH.
    Selection methods in plant breeding
    Bos, I. ; Caligari, P. - \ 2008
    Dordrecht : Springer - ISBN 9781402063695 - 461
    plantenveredeling - landbouw - populatiegenetica - populatiedynamica - selectiemethoden - plantenveredelingsmethoden - plant breeding - agriculture - population genetics - population dynamics - selection methods - plant breeding methods
    Adapt, move or perish : genetic processes in fragmented populations under climate change
    Cobben, M.M.P. ; Arens, P.F.P. ; Smulders, M.J.M. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. - \ 2007
    habitats - demografie - distributie - populatiegenetica - genetische diversiteit - klimaatverandering - simulatiemodellen - metapopulaties - ecologische hoofdstructuur - habitats - demography - distribution - population genetics - genetic diversity - climatic change - simulation models - metapopulations - ecological network
    Poster presentation of a PhD project. Which factors determine the level and distribution of genetic diversity in fragmented populations, and how are these affected by increased temperature and weather variability? METAPHOR, a stochastic, spatially explicit, individual-based simulation model for demography of fragmented populations, will be extended with a genetic module to explore these research questions
    Utilisation and conservation of farm animal genetic resources
    Oldenbroek, J.K. - \ 2007
    Wageningen : Wageningen Academic Publishers - ISBN 9789086860326 - 232
    vee - pluimvee - genetische bronnen van diersoorten - bedreigde rassen - hulpbronnengebruik - hulpbronnenbehoud - genetische diversiteit - populatiegenetica - kwantitatieve genetica - moleculaire genetica - livestock - poultry - animal genetic resources - endangered breeds - resource utilization - resource conservation - genetic diversity - population genetics - quantitative genetics - molecular genetics
    The genetic diversity comprised in farm animal species and breeds is an important resource in livestock systems. For several reasons, within the different species used for food production, only a few breeds are developed towards high-output breeds fitting in high-input systems. In this process many breeds are set aside from the food producing livestock systems. These breeds will be faced with extinction unless new functions for these breeds are found. This is a real threat for the genetic diversity within species. This book is intended to give insight into the issues of the utilisation and conservation of farm animal genetic resources towards a broad group of readers interested in these subjects. The insight is presented as applications of population, molecular and quantitative genetics that can be used to take appropriate decisions in utilisation and conservation programmes. The first two chapters discuss the decisions to be made in utilisation and conservation. Chapter 3 surveys the different ways in which the diversity we observe within a species can be characterised. Chapter 4 illustrates recent results using this theory for utilisation and conservation purposes. Chapters 5, 6 and 7 give theoretical backgrounds necessary to make decisions and chapters 8 and 9 present the operation and practical implications of selection and conservation schemes
    Population genetics of traditionally managed maize : farming practice as a determinant of genetic structure and identity of maize landraces in Mexico
    Heerwaarden, J. van - \ 2007
    Wageningen University. Promotor(en): Richard Visser; Fred van Eeuwijk. - [S.l.] : S.n. - ISBN 9789085048626 - 138
    zea mays - maïs - landrassen - genetische diversiteit - genetische erosie - landbouw bedrijven in het klein - populatiegenetica - modellen - transgene planten - mexico - zea mays - maize - landraces - genetic diversity - genetic erosion - peasant farming - population genetics - models - transgenic plants - mexico
    A large amount of crop genetic diversity is being maintained in farmers' fields worldwide. The population genetics of traditionally managed landraces is therefore of interest to the conservation of genetic resources. The growing trend towards agricultural modernization and the prospect of introducing genetically modified varieties into centers of origin have increased the need to understand the determinants of genetic structure in landraces of our basic food crops. Patterns of genetic diversity are known to be affected by environmental and geographic factors, but there has been an increasing interest in the role of farmers. Recent years have seen work on both genetic differentiation between seedlots, as well as on the agricultural practices that are expected to influence this differentiation. Unfortunately, few studies have been able to link observed patterns of differentiation to farming practice. The lack of a proper analytical framework has probably contributed to this omission. The population genetics of landraces is complex, with many human and environmental factors affecting the distribution of genetic variation. In this thesis, we aim at achieving a better understanding of the processes that underlie the genetic structure maize landraces in their centre of origin, Mexico. We combine a wide range of theoretical and empirical methods in order to provide explanations for observed patterns of genetic structure. In addition, we use these tools to predict some present and future consequences of seed management by farmers on the genetic identity of landrace populations. In chapter II, we present a metapopulation model that accounts for several features that are unique to managed maize populations. We developed a coalescence-based model of a metapopulation undergoing pollen and seed flow as well as extinction in the form of seed replacement. Unlike previous models, our model treats seed migration as episodic-, partial replacement from a single source rather than as constant immigration from the entire metapopulation. We showed that this particular form of migration leads to novel results. Contrary to classical predictions, within-deme coalescence time was not invariant to the amount of migrating seed. Genetic structure had a parabolic relationship to the amount of migrating seed instead of showing the expected exponential decrease. In contrast, the effects of seed migration frequency on diversity and structure were in line with classical predictions. We concluded that is impossible to describe seed migration by a single parameter. Genetic structure was shown to depend on deme size when the amount of migrant seed is large. Extinction decreased or increased genetic structure depending on the level of migration and number of demes. Finally, we demonstrated that higher levels of pollen migration can mask the effects of seed management. This model provides an important first step in our ability to understand the effects of farming practice on the population genetics of maize landraces. In chapter III, we study the joint role of the environment and humans as determinants of genetic differentiation. We present results on the hierarchical genetic structure in a sample of seedlots in highland and lowland environments in central Mexico. Within-and between village Fsl and Qsl values were used as measures of neutral and agronomic genetic differentiation respectively. We developed and used a new computer model to predict Fst in the two environments on the basis of data on local seed management practice and planting patterns. Strong genetic differences were found between highland and lowland maize, for both markers and traits. Three highland villages planted maize of admixed origin, as evidenced by both molecular markers and phenological traits. This suggested that human mediated gene flow from lowland to highland environments has taken place. Molecular differentiation was low for molecular markers but was notably higher in the lowlands. Our model correctly predicted this difference based on lower pollen flow and smaller seedlot sizes in the lowlands. Agronomical traits showed higher differentiation between villages and were probably subject to diversifying selection. Phenological traits showed the strongest differentiation. Field data suggested that different planting dates may explain the observed differences. Phenological differentiation was highest in the transect containing the admixed seedlots, proving that genetic structure may result from the introgression of traits that diverged in a foreign environment. In chapter IV, we address the issue of genetic erosion in modernized subsistence agriculture. Genetic erosion is thought to occur when modern varieties replace traditional landraces. Actual proof of genetic erosion for any particular area or crop has been rarely found however. A complicating factor in the study of diversity loss in traditional agriculture is the often-noted coexistence between traditional and improved varieties. Moreover, adoption of modern varieties into the traditional seed supply system may blur the distinction between modern and traditional varieties. The inability to classify germplasm into discrete types makes it hard to measure diversity. We addressed these problems by means of a case study on modernized smallholder maize agriculture in southern Mexico. We characterized seedlots obtained from both farmers and commercial seed vendors, for agronomical traits and molecular markers. Farmer interviews were used to distinguish between traditional landraces and recycled modern varieties. We calculated genetic diversity, defined as the mean differentiation between individual seedlots, for different types of germplasm. Modem germplasm was clearly distinct from traditional landraces. Close resemblance between modem- and recycled modem varieties proved that despite years of independent evolution, recycled varieties have not diverged much from their ancestral stocks. We showed that different traits reveal different levels of relative diversity, demonstrating the inherent difficulty of assessing diversity loss. The group of recycled modem varieties presented the lowest diversity for all measured traits. We could therefore predict that complete replacement of landraces by these varieties will reduce diversity in the traditional seed system. Under current patterns of coexistence however, the distinctness of modem and traditional varieties caused only a limited reduction of genetic diversity. Chapter V. deals with the effects of reproductive and population genetic processes on the probability of detecting inadvertently introduced transgenes in maize landraces. This subject has become relevant since initial findings suggesting contamination of Mexican landraces with transgenes were followed by contradictory results in subsequent years. Theoretical and simulation results showed that certain aspects of maize reproductive biology negatively affect the detection probability. We demonstrated that the strongest potential limitation on detection was caused by the aggregated frequency distribution that is a consequence of farmer-mediated introduction of transgenes. Analysis of recent sampling efforts reveals that detection probabilities may be much lower than previously assumed, partly explaining the recent inconsistent results 123
    Genetic diversity in the dutch friesian horse
    Ducro, B.J. ; Bovenhuis, H. ; Neuteboom, J.H. ; Hellinga, I. - \ 2006
    dierveredeling - paarden - paardenrassen - paardenfokkerij - stamboom - voorouders - inteelt - populatiegenetica - genetische diversiteit - fries (paardenras) - animal breeding - horses - horse breeds - horse breeding - pedigree - ancestors - inbreeding - population genetics - genetic diversity - frisian (horse breed)
    The pedigree structure of the Dutch Friesian horse breed (n=79,962) was analysed to asses the genetic diversity still present in the population. The effective number of founders explaining the genetic diversity in the reference population (i.e female horses born between 1995 and 2005) was 26, whereas the effective number of ancestors was 16. The rate of inbreeding was 1.5% per equivalent generation which is beyond the critical level of 1%. The analysis indicated that the population has suffered from a bottle-neck shortly after the establishment of the population, and that a substantial loss of allelic diversity has occurred due to drift because of small population size. The increase of average kinship during recent generations has declined and this coincided with a substantial growth of the population. A decline of the rate of inbreeding might be expected, but a proper conservation programme is still needed to further reduce allelic loss from the population
    Genetic diversity within and between European pig breeds using microsatellite markers
    SanCristobal, M. ; Chevalet, C. ; Haley, C.S. ; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. - \ 2006
    Animal Genetics 37 (2006)3. - ISSN 0268-9146 - p. 189 - 198.
    dierveredeling - varkens - wilde varkens - varkensrassen - conservering - rasverschillen - biodiversiteit - genetische afstand - genetische diversiteit - genetische merkers - heterozygotie - allelen - microsatellieten - populatiegenetica - statistische analyse - animal breeding - pigs - wild pigs - pig breeds - conservation - breed differences - biodiversity - genetic distance - genetic diversity - genetic markers - heterozygosity - alleles - microsatellites - population genetics - statistical analysis - populations - evolution - humans - loci - distance
    An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43–0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy–Weinberg expectations (P <0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright FST index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.
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