Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

    Current refinement(s):

    Records 1 - 20 / 23

    • help
    • print

      Print search results

    • export

      Export search results

    Check title to add to marked list
    Population-level consequences of complementary sex determination in a solitary parasitoid
    Boer, J.G. de; Groenen, M.A.M. ; Pannebakker, B.A. ; Beukeboom, L.W. ; Kraus, R.H.S. - \ 2015
    BMC Evolutionary Biology 15 (2015). - ISSN 1471-2148 - 11 p.
    biological-control introduction - multilocus genotype data - wasp cotesia-glomerata - bee apis-mellifera - genetic-structure - linkage analysis - mating system - diploid males - determination mechanisms - ascertainment bias
    BACKGROUND: Sex determination mechanisms are known to be evolutionarily labile but the factors driving transitions in sex determination mechanisms are poorly understood. All insects of the Hymenoptera are haplodiploid, with males normally developing from unfertilized haploid eggs. Under complementary sex determination (CSD), diploid males can be produced from fertilized eggs that are homozygous at the sex locus. Diploid males have near-zero fitness and thus represent a genetic load, which is especially severe under inbreeding. Here, we study mating structure and sex determination in the parasitoid Cotesia vestalis to investigate what may have driven the evolution of two complementary sex determination loci in this species. RESULTS: We genotyped Cotesia vestalis females collected from eight fields in four townships in Western Taiwan. 98 SNP markers were developed by aligning Illumina sequence reads of pooled DNA of eight different females against a de novo assembled genome of C. vestalis. This proved to be an efficient method for this non-model species and provides a resource for future use in related species. We found significant genetic differentiation within the sampled population but variation could not be attributed to sampling locations by AMOVA. Non-random mating was detected, with 8.1% of matings between siblings. Diploid males, detected by flow cytometry, were produced at a rate of 1.4% among diploids. CONCLUSIONS: We think that the low rate of diploid male production is best explained by a CSD system with two independent sex loci, supporting laboratory findings on the same species. Fitness costs of diploid males in C. vestalis are high because diploid males can mate with females and produce infertile triploid offspring. This severe fitness cost of diploid males combined with non-random mating may have resulted in evolution from single locus CSD to CSD with two independent loci
    Interplay of robustness and plasticity of life history traits in habitats with different thermal regimes
    Liefting, M. ; Grunsven, R.H.A. van; Morrissey, M.B.M. ; Timmermans, M. ; Ellers, J. - \ 2015
    Journal of Evolutionary Biology 28 (2015)5. - ISSN 1010-061X - p. 1057 - 1066.
    orchesella-cincta collembola - wild bird population - phenotypic plasticity - reaction norms - genetic-structure - environmental canalization - drosophila-melanogaster - indeterminate growth - soil arthropod - evolution
    Phenotypic plasticity describes the ability of an individual to alter its phenotype in response to the environment and is potentially adaptive when dealing with environmental variation. However, robustness in the face of a changing environment may often be beneficial for traits that are tightly linked to fitness. We hypothesized that robustness of some traits may depend on specific patterns of plasticity within and among other traits. We used a reaction norm approach to study robustness and phenotypic plasticity of three life-history traits of the collembolan Orchesella cincta in environments with different thermal regimes. We measured adult mass, age at maturity and growth rate of males and females from heath and forest habitats at two temperatures (12 and 22 °C). We found evidence for ecotype-specific robustness of female adult mass to temperature, with a higher level of robustness in the heath ecotype. This robustness is facilitated by plastic adjustments of growth rate and age at maturity. Furthermore, female fecundity is strongly influenced by female adult mass, explaining the importance of realizing a high mass across temperatures for females. These findings indicate that different predicted outcomes of life-history theory can be combined within one species' ontogeny and that models describing life-history strategies should not assume that traits like growth rate are maximized under all conditions. On a methodological note, we report a systematic inflation of variation when standard deviations and correlation coefficients are calculated from family means as opposed to individual data within a family structure.
    Traditional land use and reconsideration of environmental zoning in the Hawf Protected Area, south-eastern Yemen
    Slecht, E. ; Zaballos, L.G.H. ; Quiroz Villarreal, D.K. ; Scholte, P. ; Buerkert, A. - \ 2014
    Journal of Arid Environments 109 (2014). - ISSN 0140-1963 - p. 92 - 102.
    monsoonal fog oases - arabian peninsula - mountain pastures - genetic-structure - conservation - goats - populations - forest - kenya
    The Al Hawf area at the Yemen–Oman border hosts a unique fog-derived ecosystem which, due to its high diversity of plant and animal species, merits protection. Given the area's remoteness, poor infrastructure, high population growth and limited exchanges across the Omani border, the local livelihoods strongly rely on the exploitation of natural marine and terrestrial resources. Since quantitative data on the intensity of anthropogenic pressure on the terrestrial ecosystem are lacking, the present study analysed the impact of agricultural and pastoral land use on the vegetation of the designated Hawf Protected Area (HPA). To this end structured interviews, village walks and other rural appraisal tools were combined with vegetation surveys and GPS-based monitoring of pasturing livestock herds. The loss of traditional herding systems that regulated selective management of fragile grazing grounds along the altitude gradient in the HPA, particularly for camels, the overexploitation of woody perennials for construction purposes, and the resettlement of former migrant workers are major constraints for the successful implementation of the government-designed management plan. Implementation could be improved by better taking into account the vegetation composition in the area, current and traditional grazing schemes and local people's needs for off-farm income
    The domestication and evolutionary ecology of apples
    Cornille, A. ; Giraud, T. ; Smulders, M.J.M. ; Roldán-Ruiz, I. ; Gladieux, P. - \ 2014
    Trends in Genetics 30 (2014)2. - ISSN 0168-9525 - p. 57 - 65.
    wild malus-orientalis - genetic-structure - population-structure - venturia-inaequalis - crop domestication - cultivated apple - fruit - sylvestris - markers - mill.
    The cultivated apple is a major fruit crop in temperate zones. Its wild relatives, distributed across temperate Eurasia and growing in diverse habitats, represent potentially useful sources of diversity for apple breeding. We review here the most recent findings on the genetics and ecology of apple domestication and its impact on wild apples. Genetic analyses have revealed a Central Asian origin for cultivated apple, together with an unexpectedly large secondary contribution from the European crabapple. Wild apple species display strong population structures and high levels of introgression from domesticated apple, and this may threaten their genetic integrity. Recent research has revealed a major role of hybridization in the domestication of the cultivated apple and has highlighted the value of apple as an ideal model for unraveling adaptive diversification processes in perennial fruit crops. We discuss the implications of this knowledge for apple breeding and for the conservation of wild apples.
    Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon
    Banaticla-Hilario, M.C.N. ; Berg, R.G. van den; Hamilton, N.R.S. ; McNally, K.L. - \ 2013
    Ecology and Evolution 3 (2013)9. - ISSN 2045-7758 - p. 3047 - 3062.
    asian wild-rice - multilocus genotype data - cultivated rice - population-structure - genetic-structure - phylogenetic analysis - evolutionary relationships - insertion-polymorphism - island populations - species cohesion
    Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F-ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H-E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H-E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
    On the asymmetry of mating in natural populations of the mushroom fungus Schizophyllum commune
    Nieuwenhuis, B.P.S. ; Nieuwhof, S. ; Aanen, D.K. - \ 2013
    Fungal Genetics and Biology 56 (2013). - ISSN 1087-1845 - p. 25 - 32.
    cut beech logs - incompatibility factors - nuclear migration - heterobasidion-annosum - mitochondrial genome - buller phenomenon - genetic-structure - dna - inheritance - selection
    Before a mycelium of a mushroom-forming basidiomycete develops mushrooms, the monokaryotic mycelium needs to become fertilized. Although the mechanistic details of mating in mushrooms have been studied thoroughly in laboratory research, very little is known on mating patterns in nature. In this study, we performed fine-scale analyses of three populations of Schizophyllum commune from their natural substrate (i.e. dead beech branches). From the three branches, 24, 12, and 24 fruiting bodies were isolated and for each mushroom, the origins of its nuclei and cytoplasm were reconstructed using DNA markers. Nuclear genotypes were determined using sequencing data and mating types, and mitochondrial haplotypes using SNP markers. From these combined data we reconstructed colonization and mating patterns of the mycelia. On each branch, we found multiple dikaryons (3, 3, and 8, respectively); in two instances one nuclear haplotype was shared between two dikaryons and in two other cases a nuclear haplotype was shared between three dikaryons. Each dikaryon always had a single mitochondrial haplotype. These findings indicate that mating usually is not symmetrical and that a monokaryon is most likely fertilized by a small monokaryon, a spore or a dikaryon. Sharing of nuclear haplotype between different dikaryons resulted either from multiple fertilizations of a single monokaryon, if the dikaryons had identical mitochondrial haplotypes, or, if the dikaryons had different mitochondria] haplotypes, most likely from secondary matings between a monokaryon and a dikaryon (Buller phenomenon). We conclude that mating in S. commune between same-sized monokaryons with reciprocal migration, as generally described in textbooks, is rare in nature. We discuss the implications of non-symmetric mating for basidiomycete evolution. (C) 2013 Elsevier Inc. All rights reserved.
    Ecogeographic variation in the morphology of two Asian wild rice species Oryza nivara and O. ruftipogon.
    Banaticla, M.C.N. ; Sosef, M.S.M. ; McNally, K.L. ; Sackville Hamilton, R. ; Berg, R.G. van den - \ 2013
    International Journal of Plant Sciences 174 (2013)6. - ISSN 1058-5893 - p. 896 - 909.
    genetic-structure - genus oryza - phylogenetic-relationships - evolutionary relationships - o-rufipogon - populations - diversity - perennis - sativa - differentiation
    To search for variation patterns and diagnostic features between Asian wild rice species, several numerical methods were applied to phenotypic data obtained from 116 accessions representing sympatric populations of Oryza nivara and Oryza rufipogon from tropical continental Asia and O. rufipogon populations from insular Southeast Asia and Australasia. Ordination and cluster analyses separate O. rufipogon from O. nivara, indicating the presence of two sympatric morphological species occupying different ecological niches. Oryza nivara and O. rufipogon are morphologically more differentiated in South Asia than in mainland Southeast Asia, implying more recent divergence and/or more interspecific gene flow among sympatric populations in the latter region. Oryza nivara exhibits South and Southeast Asian phenotypes while the Australasian populations of O. rufipogon appear as distinct from the rest of the species. Seedling height, culm number, and diameter; leaf length and width; and anther length were significantly correlated to certain geoclimatic factors and displayed contrasting correlation directions for O. nivara and O. rufipogon, implying that the two species respond differently to geographic and climatic gradients. Diagnostic characters are provided to delineate the species morphologically. The results suggest the strong influence of ecology on species morphology, existence of geographic races within species and morphological divergence between O. nivara and O. rufipogon.
    Improving hierarchical clustering of genotypic data via principal component analysis
    Odong, T.L. ; Heerwaarden, J. van; Hintum, T.J.L. van; Eeuwijk, F.A. van; Jansen, J. - \ 2013
    Crop Science 53 (2013). - ISSN 0011-183X - p. 1546 - 1554.
    genome-wide association - molecular marker data - genetic-structure - core collections
    Understanding the genetic structure of germplasm collections is a prerequisite for effective and efficient use of crop genetic resources in genebanks. Currently, hierarchical clustering techniques are most popular for describing genetic structure in germplasm collections. Traditionally performed using dissimilarities based on raw genotypic data, recent studies have shown that cluster analysis can be improved by first condensing the genotypic data using principal component analysis (PCA). Although the two-step approach (PCA followed by cluster analysis) is gaining popularity, no systematic study into its benefits over traditional clustering methods has been performed. In particular, the relationship between the number of principal components (PCs) to be retained and the performance of cluster analysis have not been established. It is also not clear whether genetic data should be scaled before performing PCA. Here we present a detailed study comparing cluster analysis using distances based on condensed data using significant PCs and clustering based on the full dataset. We also studied the effect of data scaling on PCA-based clustering. Using simulations, we show that in discretely subdivided populations, maximum clustering performance is attained by using a subset of PCs that relate to differentiation between subpopulations and that scaling of the data is key to achieving improvement in PCA-based clustering. For scaled data, we report consistently higher clustering success for PCA, particularly at lower levels of population differentiation, while gains for unscaled data are minor. This is confirmed by real data, where PCA-based clustering of scaled genotypic data leads to visible improvements in resolving finer patterns of geographic subdivision. Our results show clearly that proper scaling and reduction of genotypic data is key to improving clustering performance
    Characterisation of Phytophthora infestans Isolates Collected from Potato and Tomato Crops in Tunisia During 2006–2008
    Harbaoui, K. ; Lee, T.A.J. van der; Vleeshouwers, V.G.A.A. ; Khammassy, N. ; Harrabi, M. ; Hamada, W. - \ 2013
    Potato Research 56 (2013)1. - ISSN 0014-3065 - p. 11 - 29.
    genotypic diversity - united-states - mating-type - northwestern washington - genetic-structure - populations - resistance - metalaxyl - migration - canada
    Severe late blight epidemics in Tunisia in recent years prompted population studies on the pathogen responsible for this disease, Phythophthora infestans. Characterisation of 165 Tunisian P. infestans isolates collected from 2006 to 2008 was performed for the mating type and mt haplotype, while subsets were analysed for metalaxyl sensitivity (n¿=¿65), virulence on differential set of 11 R genes of Solanum demissum (n¿=¿31), aggressiveness on cv. Bintje (n¿=¿36) and measurement of the radial growth on agar medium at three temperatures (n¿=¿38). Most isolates from potato and all isolates from tomato had the A1 mating type. The A2 mating type was detected in the north-east and northern areas, but not in the north-west. All the A2 mating type isolates were metalaxyl resistant and seem to be part of a new generation of the P. infestans isolates which are more aggressive, with more complex races, and tolerant to higher temperatures. The increased severity of epidemics during 2006 to 2008 can be attributed to favourable weather conditions during growing seasons, adaptation of new genotypes, widespread phenylamide resistance in potato production regions and most probably incorrect spray programmes. In contrast to the presence of complex pathotypes in two major potato crop regions (north-east and northern areas), the P. infestans population detected in the other regions and in tomato crops was still relatively simple. Compared with the situation in Europe and the American continent, or even compared with neighbouring countries such as Algeria, the genetic changes in Tunisia are still comforting and require strict management decision on late blight control to avoid the spread of new P. infestans populations from Europe or neighbouring countries
    Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms
    Kraus, R.H.S. ; Hooft, W.F. van; Megens, H.J.W.C. ; Tsvey, A. ; Fokin, S.Y. ; Ydenberg, R.C. ; Prins, H.H.T. - \ 2013
    Molecular Ecology 22 (2013)1. - ISSN 0962-1083 - p. 41 - 55.
    maximum-likelihood-estimation - mallard anas-platyrhynchos - influenza-a viruses - population-structure - mitochondrial-dna - phylogenetic networks - coalescent approach - genetic-structure - biased dispersal - white sharks
    Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.
    Strong persistent growth differences govern individual performance and population dynamics in a tropical forest understorey palm
    Jansen, M. ; Zuidema, P.A. ; Anten, N.P.R. ; Martínez-Ramos, M. - \ 2012
    Journal of Ecology 100 (2012)5. - ISSN 0022-0477 - p. 1224 - 1232.
    neotropical rain-forest - astrocaryum-mexicanum - genetic-structure - life-histories - model - size - variability - patterns - trees - age
    1. Persistent variation in growth rate between individual plants can have strong effects on population dynamics as fast growers reach the reproductive size at an earlier age and thus potentially contribute more to population growth than slow growers. In tropical forests, such persistent growth differences have so far been documented for canopy tree species, where they are primarily associated with forest gap dynamics, but not for forest understorey species which are less responsive to gaps. Here, we study persistent growth differences and their demographic consequences for a tropical forest understorey palm, Chamaedorea elegans. 2. We measured internodes along stems and annual leaf production rates to reconstruct lifetime growth trajectories. Using regression analysis, we determined the relative effect of stem length and past growth rate on vital rates (survival, growth and reproduction). We then simulated population dynamics using integral projection models (IPMs), in which individuals were categorized by both stem length and lifetime past growth rate. 3. Stem growth differences among individual palms persisted over most of their lifetime. Past growth rate averaged over the palm’s lifetime proved to be a very good predictor of growth, reproduction probability and seed production, often much better than stem length or age. The effects of past growth rate were positive, indicating that fast growers maintain high rates of growth and reproduction. 4. Projected population growth rate (k) was 1.056, and stable stage distributions closely resembled observed population structures. Separating individuals with above-median and below-median past growth rates in IPMs revealed substantial differences in elasticity values. The 50% fastest growers had a 1.8 times higher elasticity, and thus a 1.8 times higher contribution to population growth, compared to slow growers. 5. Synthesis. Strong and persistent growth differences that are probably associated with environmental (edaphic) and/or genetic factors govern individual performance and population dynamics of a tropical forest understorey palm. Overall, our study shows that strong inter-individual growth variation is not limited to canopy trees and that it can be generated by other factors than canopy dynamics. It is likely that persistently fast-growing ‘super performers’ govern population growth of many long-lived species.
    Pepino mosaic virus isolates and differential symptomatology in tomato
    Hanssen, I.M. ; Paeleman, A. ; Vandewoestijne, E. ; Bergen, L. Van; Bragard, C. ; Lievens, B. ; Vanachter, A.C.R.C. ; Thomma, B.P.H.J. - \ 2009
    Plant Pathology 58 (2009)3. - ISSN 0032-0862 - p. 450 - 460.
    genomic rna - genetic-structure - sequence - protein - replication - variability - population - distinct - quality - strain
    Based on a survey conducted in commercial tomato production in Belgium in 2006, four Pepino mosaic virus (PepMV) isolates that differed in symptom expression in the crop of origin were selected for greenhouse trials. The selected isolates were inoculated onto tomato plants grown in four separate plastic tunnels. PepMV symptom development was assessed regularly and extensive sampling followed by ELISA analyses, genotyping and sequencing was performed to study viral presence and variation in PepMV sequences throughout the trial period. Two isolates (EU-mild and CH2-mild) that were selected based on mild symptom expression in the crop of origin caused only mild symptoms in the trial, while two other isolates (CH2-aggressive and EU + CH2) that were selected for severe symptom display, caused considerably more severe symptoms. Sequence homology between CH2-mild and CH2-aggressive was as high as 99·4%. Results of this study show that differential symptom expression can, at least partially, be attributed to the PepMV isolate, which may be related to minor differences at the nucleotide level between isolates.
    Pollinator networks, alien species and the conservation of rare plants: Trinia glauca as a case study
    Carvalheiro, L.G. ; Barbosa, E.R. ; Memmott, J. - \ 2008
    Journal of Applied Ecology 45 (2008)5. - ISSN 0021-8901 - p. 1419 - 1427.
    genetic-structure - food webs - pollen - ants - fragmentation - consequences - population - robustness - complexity - system
    1. Despite the essential role of pollination in the maintenance of many rare plant species, conservation management plans rarely consider the service of pollination. 2. This study identifies the main pollinators of a rare English plant species, Trinia glauca (Apiaceae), and provides recommendations for its conservation. A community-level approach is used, whereby a visitation network is constructed to identify the direct and indirect links between T. glauca and other members of the plant-visitor community. 3. A field experiment that excluded the main visitor species from female T. glauca showed that ants were the main pollinators of T. glauca. The network revealed that over the field season, 33% of the ants' visits to flowers were to alien plants, with Cotoneaster horizontalis making a particularly high contribution (58%) during the T. glauca flowering period. 4. The removal of alien plants is a part of the conservation management of T. glauca, and we simulated the likely consequences of this form of habitat management on T. glauca pollination, any effects being mediated by shared pollinators. Although positive or neutral effects are possible, a negative effect is also possible, whereby the removal of alien plants leads to a crash in ant populations, potentially reducing pollinator visits to T. glauca by up to 85.2%. 5. Synthesis and applications. Conserving the pollinators of rare plants is essential if their conservation is to be sustainable in the long term. Our data indicate that T. glauca is pollinated by ants and demonstrate that ants can also feed on alien plants, particularly during the flowering season of this rare plant. We suggest that management measures involving the removal of alien plants should consider the possible negative impacts on rare plants through changes in pollinator populations. In this case, a staged removal is likely to prove the best conservation approach, allowing the pollinators' response to be assessed before any serious negative effects occur.
    Indirect evidence for sexual reproduction in Cercospora beticola populations from sugar beet
    Groenewald, M. ; Linde, C.C. ; Groenewald, J.Z. ; Crous, P.W. - \ 2008
    Plant Pathology 57 (2008)1. - ISSN 0032-0862 - p. 25 - 32.
    pathogen mycosphaerella-graminicola - leaf-spot - mating-type - fusarium-oxysporum - genetic-structure - fungi - diversity - dna - recombination - maize
    Cercospora beticola is the main causal agent of cercospora leaf spot on sugar beet and has a large negative impact on the yield and quality of sugar beet production worldwide. Previous studies have shown that both mating type idiomorphs of C. beticola are present in natural populations, suggesting that C. beticola is heterothallic and may be reproducing sexually. Cercospora beticola isolates are diverse in the morphology of their conidia, onset of disease symptoms and fungicide resistance. To find the source of this diversity and to determine if sexual reproduction occurs in this fungus, C. beticola populations were collected from Western Europe, Iran and New Zealand. The mating types of these isolates were determined and AFLP analyses were used to study the genetic diversity in these populations. The mating type ratios did not deviate significantly from a 1:1 ratio in most of the populations and AFLP analyses showed high levels of genetic variation within and between the populations, with 86.4% of the isolates having unique genotypes. All populations were in significant linkage disequilibrium but levels of disequilibrium were low, and loci from only one primer pair were in significant gametic equilibrium in populations from the Netherlands and Italy. From these results there is the possibility that C. beticola reproduces sexually. High levels of gene flow among the samples from Europe demonstrated a single panmictic European population. This study confirms C. beticola to be a genetically highly diverse species, supporting the assumption that some populations are reproducing sexually.
    Intraspecific comparison of the mitochondrial genome sequences from two strains of the plant pathogenic fungus Mycosphaerella graminicola
    Torriani, S.F.F. ; Goodwin, S.B. ; Kema, G.H.J. ; McDonald, B.A. - \ 2008
    Fungal Genetics and Biology 45 (2008)5. - ISSN 1087-1845 - p. 628 - 637.
    fragment-length-polymorphism - septoria-tritici blotch - complete dna-sequence - genetic-structure - nuclear - diversity - wheat - populations - evolution - selection
    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of 35 additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.
    Population structure and historical demography of the thorny skate (Amblyraja radiata, Rajidae) in the North Atlantic
    Chevolot, M. ; Wolfs, P.H.J. ; Palsson, J. ; Rijnsdorp, A.D. ; Stam, W.T. ; Olsen, J.L. - \ 2007
    Marine Biology 151 (2007)4. - ISSN 0025-3162 - p. 1275 - 1286.
    pleuronectes-platessa l. - ray raja-clavata - mitochondrial-dna - baltic sea - geographical-distribution - cladistic-analysis - secondary contact - genetic-structure - english-channel - fucus-serratus
    Population genetic structure of the thorny skate (Amblyraja radiata) was surveyed in >300 individuals sampled from Newfoundland, Iceland, Norway, the Kattegat and the central North Sea. A 290-bp fragment of the mt cytochrome-b gene was first screened by SSCP. Sequences of SSCP haplotypes revealed 34 haplotypes, 14 of which were unique to Iceland, 3 to Newfoundland, 1 to Norway and 3 to the Kattegat. The global F ST was weak but significant. Removal of the two Kattegat locations, which were the most differentiated, resulted in no significant genetic differentiation. Haplotype diversity was high and evenly distributed across the entire Atlantic (h = 0.8) with the exception of the North Sea (h = 0.48). Statistical parsimony revealed a star-like genealogy with a central widespread haplotype. A subsequent nested clade analysis led to the inference of contiguous expansion with evidence for long distance dispersal between Newfoundland and Iceland. Historical demographic analysis showed that thorny skates have undergone exponential population expansion that started between 1.1 million and 690,000 years ago; and that the Last Glacial Maximum apparently had little effect. These results strongly differ from those of a parallel study of the thornback ray (Raja clavata) in which clear structure and former refugial areas could be identified. Although both species have similar life history traits and overlapping ranges, the continental shelf edge apparently does not present a barrier to migration in A. radiata, as it does for R. clavata
    Isolation and characterization of the mating type locus of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana
    Conde, L. ; Waalwijk, C. ; Canto-Canché, B.B. ; Kema, G.H.J. ; Crous, P.W. ; James, A.C. ; Abeln, E.C.A. - \ 2007
    Molecular Plant Pathology 8 (2007)1. - ISSN 1464-6722 - p. 111 - 120.
    septoria-passerinii - genetic-structure - fungal pathogen - ribosomal dna - graminicola - wheat - idiomorphs - sigatoka - cloning - region
    Idiomorphs mat1-1 and mat1-2 from Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana, were isolated. Degenerate oligos were used to amplify the HMG box of the mat1-2 idiomorph from M. fijiensis, showing homology with the HMG box of Mycosphaerella graminicola. Using a DNA walking strategy, anchored on the DNA lyase gene towards the HMG box, a 9-kb-long region of mat1-2 was obtained. A 5-kb fragment from the mat1-1 region was obtained by long-range PCR using primers on the flanking regions, which have close to 100% identity between both idiomorphs. High-identity (77¿89%), inverted regions within both idiomorphs were found, which suggest unique inversion events, which have not been found before, and that could have been significant in the evolution of this species. The predicted genes showed the conserved introns in both idiomorphs as well as an additional intron within the alpha box. The implications for the evolution of species in the Mycosphaerella complex on banana are discussed
    Phylogeography and population structure of thornback rays (Raja clavata L., Rajidae)
    Chevolot, M. ; Hoarau, G. ; Rijnsdorp, A.D. ; Stam, W.T. - \ 2006
    Molecular Ecology 15 (2006)12. - ISSN 0962-1083 - p. 3693 - 3705.
    pleuronectes-platessa l. - genetic-structure - north-sea - english-channel - geographical-distribution - secondary contact - fucus-serratus - f-statistics - ice-age - dna
    The phylogeography of thornback rays (Raja clavata) was assessed from European waters, using five nuclear microsatellite loci and mitochondrial cytochome b sequences. Strong regional differentiation was found between the Mediterranean basin, the Azores and the European continental shelf. Allelic and haplotype diversities were high in Portuguese populations, consistent with the existence of a refugium along the Iberian Peninsula. Unexpectedly, high diversity was also found in the English Channel/North Sea area. The lowest genetic diversity was found in the Black Sea. Populations sampled from the Mediterranean, Adriatic and Black Seas were characterized by a single mitochondrial haplotype. This haplotype was also the most ancestral and widespread outside of the Mediterranean basin except for the Azores. Populations from the Azores were dominated by a second ancestral haplotype which was shared with British populations. Results from multidimensional scaling, amova and nested clade analysis indicate that British waters are a secondary contact zone recolonized from at least two refugia ¿ one around the Iberian Peninsula and one possibly in the Azores. Links to a potential refugium known as the Hurd Deep, between Cornwall and Brittany, are discussed. Finally, a historical demographic analysis indicates that thornback ray populations started to expand between 580 000 and 362 000 years ago, which suggests that the Last Glacial Maximum (20 000 years ago) had mainly affected the distribution of populations rather than population size
    Population structure of the thornback ray (Raja clavata L.) in British waters
    Chevolot, M. ; Ellis, J.R. ; Hoarau, G. ; Rijnsdorp, A.D. ; Stam, W.T. ; Olsen, J.L. - \ 2006
    Journal of Sea Research 56 (2006)4. - ISSN 1385-1101 - p. 305 - 316.
    cod gadus-morhua - pleuronectes-platessa l. - southern north-sea - gulf-of-mexico - genetic-structure - atlantic cod - multilocus genotypes - microsatellite data - geographic scales - reaction norms
    Prior to the 1950s, thornback ray (Raja clavata L.) was common and widely distributed in the seas of Northwest Europe. Since then, it has decreased in abundance and geographic range due to over-fishing. The sustainability of ray populations is of concern to fisheries management because their slow growth rate, late maturity and low fecundity make them susceptible to exploitation as victims of by-catch. We investigated the population genetic structure of thornback rays from 14 locations in the southern North Sea, English Channel and Irish Sea. Adults comprised <4% of the total sampling despite heavy sampling effort over 47 hauls; thus our results apply mainly to sexually immature individuals. Using five microsatellite loci, weak but significant population differentiation was detected with a global FST = 0.013 (P <0.001). Pairwise Fst was significant for 75 out of 171 comparisons. Although earlier tagging studies suggest restricted foraging distances from home areas, the absence of genetic differentiation between some distant populations suggests that a substantial fraction of individuals migrate over wide areas. Autumn/winter locations appear to have a lower level of differentiation than spring/summer, which could be due to seasonal migration. Management and conservation of thornback ray populations will be challenging as population structure appears to be dynamic in space and time
    Evidence for natural selection in the mitochondrial genome of Mycosphaerella graminicola
    Zhan, J. ; Kema, G.H.J. - \ 2004
    Phytopathology 94 (2004)3. - ISSN 0031-949X - p. 261 - 267.
    fragment-length-polymorphisms - anamorph-septoria-tritici - in-field populations - genetic-structure - sexual reproduction - cryphonectria-parasitica - stagonospora-nodorum - pyricularia-grisea - agaricus-bisporus - host-specificity
    Pathogenicity assays were combined with restriction fragment length polymorphism (RFLP) markers in the mitochondrial and nuclear genomes to compare Mycosphaerella grominicola populations adapted to bread wheat (Triticum aestivum) and durum wheat (T. turgidum) in the Mediterranean Basin. The majority of isolates had unique nuclear DNA fingerprints and multilocus haplotypes. Only six mitochondrial DNA (mtDNA) haplotypes were identified among 108 isolates assayed. There were minor differences in frequencies of alleles at nuclear RFLP loci between the two host-adapted populations, but differences in the frequencies of mtDNA haplotypes were highly significant (P <0.0001). mtDNA haplotype I dominated on the isolates adapted to bread wheat, and its frequency was twice as high as for the isolates adapted to durum wheat. mtDNA haplotype 4. which contained a unique approximate to3-kb insertion, was detected only in isolates showing specificity toward durum wheat and was the dominant haplotype on this species. We propose that the low mitochondrial diversity in this pathogenic fungus is due to a selective sweep and that differences in the frequencies of mtDNA haplotypes between the two host-adapted populations, were due to natural selection according, to host species.
    Check title to add to marked list
    << previous | next >>

    Show 20 50 100 records per page

     
    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.