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.

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    On the evolution of azole resistance in Aspergillus fumigatus
    Zhang, J. - \ 2016
    Wageningen University. Promotor(en): Bas Zwaan; P.E. Verweij, co-promotor(en): Fons Debets; Sijmen Schoustra. - Wageningen : Wageningen University - ISBN 9789462578555 - 183
    aspergillus fumigatus - azoles - triazoles - aspergillosis - resistance - life cycle - asexual reproduction - sexual reproduction - experimental evolution - evolutionary genetics - agriculture - composting - medicine - aspergillus fumigatus - azolen - triazolen - aspergillose - weerstand - levenscyclus - ongeslachtelijke voortplanting - geslachtelijke voortplanting - experimentele evolutie - evolutionaire genetica - landbouw - compostering - geneeskunde

    During the last decade azole resistance has increasingly been reported in Aspergillus fumigatus, which is a fungal pathogen involved in the vast majority of invasive aspergillosis infections in humans, and is now a global public health concern. Antifungal azoles, especially triazoles, are the drugs of choice for medical treatment. However, this treatment is hampered by the emergence of multi-azole resistant A. fumigatus isolates, especially the highly resistant variants TR34/L98H and TR46 /Y121F/T289A. Therefore, to control this disease, it is essential to elucidate by what mechanisms resistance emerges, how resistance spreads and how resistant genotypes persist in environments without azoles. The presented thesis shows the relevance of the life cycle of A. fumigatus to the development of azole resistance and possible evolutionary routes that lead to it. The work highlights the importance of fungal biology and evolution towards understanding the development of azole resistance in fungi. We conclude that azole resistance in A. fumigatus is a consequence of selection pressure by azole in the environment on the genetic variation generated via various aspects in the A. fumigatus life cycle. This thesis also introduces an experimental evolution approach to study the dynamics and mechanisms of the evolution of azole resistance. In addition, we investigate what condition can lead an environment to be a possible hotspot for the development of resistance. Finally, we link this to the potential conditions under which resistance can emerge and spread in the lungs of humans and how this depends on the specific azole used.

    Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus
    Lin, K. ; Limpens, E.H.M. ; Zhang, Z. ; Ivanov, S. ; Saunders, D.G.O. ; Mu, D. ; Pang, E. ; Cao, H. ; Cha, H. ; Lin, T. ; Zhou, Q. ; Shang, Y. ; Li, Y. ; Sharma, T.C. ; Velzen, R. van; Ruijter, N.C.A. de; Aanen, D.K. ; Win, J. ; Kamoun, S. ; Bisseling, T. ; Geurts, R. ; Huang, S.W. - \ 2014
    Plos Genetics 10 (2014)1. - ISSN 1553-7404 - 13 p.
    arbuscular mycorrhizal fungi - pathogen phytophthora-infestans - glomus-intraradices - sexual reproduction - protein families - cdna sequences - kingdom fungi - gene - identification - efficient
    Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
    The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution
    Bolton, M.D. ; Jonge, R. de; Inderbitzin, P. ; Liu, Z. ; Birla, K. ; Peer, Y. Van de; Subbarao, K. ; Thomma, B.P.H.J. ; Secor, G. - \ 2014
    Fungal Genetics and Biology 62 (2014). - ISSN 1087-1845 - p. 43 - 54.
    de-novo identification - sexual reproduction - neurospora-tetrasperma - molecular-organization - fungal pathogens - loci - systems - recombination - resistance - tool
    Dothideomycetes is one of the most ecologically diverse and economically important classes of fungi. Sexual reproduction in this group is governed by mating type (MAT) genes at the MAT1 locus. Self-sterile (heterothallic) species contain one of two genes at MAT1 (MAT1-1-1 or MAT1-2-1) and only isolates of opposite mating type are sexually compatible. In contrast, self-fertile (homothallic) species contain both MAT genes at MAT1. Knowledge of the reproductive capacities of plant pathogens are of particular interest because recombining populations tend to be more difficult to manage in agricultural settings. In this study, we sequenced MAT1 in the heterothallic Dothideomycete fungus Cercospora beticola to gain insight into the reproductive capabilities of this important plant pathogen. In addition to the expected MAT gene at MAT1, each isolate contained fragments of both MAT1-1-1 and MAT1-2-1 at ostensibly random loci across the genome. When MAT fragments from each locus were manually assembled, they reconstituted MAT1-1-1 and MAT1-2-1 exons with high identity, suggesting a retroposition event occurred in a homothallic ancestor in which both MAT genes were fused. The genome sequences of related taxa revealed that MAT gene fragment pattern of Cercospora zeae-maydis was analogous to C. beticola. In contrast, the genome of more distantly related Mycosphaerella graminicola did not contain MAT fragments. Although fragments occurred in syntenic regions of the C. beticola and C. zeae-maydis genomes, each MAT fragment was more closely related to the intact MAT gene of the same species. Taken together, these data suggest MAT genes fragmented after divergence of M. graminicola from the remaining taxa, and concerted evolution functioned to homogenize MAT fragments and MAT genes in each species.
    Control of Pig Reproduction IX
    Rodriguez-Martinez, H. ; Soede, N.M. ; Flowers, W.L. - \ 2013
    Leicestershire, United Kingdom : Context Products Ltd (Society of Reproduction and Fertility volume 68) - ISBN 9781899043484 - 345
    varkens - geslachtelijke voortplanting - gameten - embryo's - kunstmatige inseminatie - embryotransplantatie - zwangerschap - partus - pasgeborenen - biggen - overleving - biotechnologie - metabolomica - eiwitexpressieanalyse - kunstmatige selectie - pigs - sexual reproduction - gametes - embryos - artificial insemination - embryo transfer - pregnancy - parturition - neonates - piglets - survival - biotechnology - metabolomics - proteomics - artificial selection
    Snow shoes and sandals? : genetic aspects of heat stress sensitivity and sow reproduction
    Bloemhof, S. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk; I. Misztal, co-promotor(en): E.F. Knol; Liesbeth van der Waaij. - S.l. : s.n. - ISBN 9789461735881 - 173
    zeugen - warmtestress - diergenetica - gevoeligheid - geslachtelijke voortplanting - voortplantingsvermogen - kritische temperatuur - hittetolerantie - selectief fokken - genetische correlatie - veredelingsprogramma's - varkensfokkerij - sows - heat stress - animal genetics - sensitivity - sexual reproduction - reproductive performance - critical temperature - heat tolerance - selective breeding - genetic correlation - breeding programmes - pig breeding

    Globally the average size of pig herds are increasing and amount of labour spent per sow / finisher pig is decreasing. These changes require sows which need less management interventions. In addition to easier manageable sows modern genotypes will also need to be more adaptable considering that global temperatures are expected to increase and pork production is partially moving to warmer climates. The end result is that commercial pigs nowadays will potentially face more heat stress challenges during their productive lives.

    In this thesis, a model was developed which was used to estimate upper critical temperatures for sows’ reproductive performance. Additionally the possibility to breed for reduced heat tolerance of sows was investigated. Therefore heritability for the random regression slope of farrowing rate against increasing temperature at day of insemination (= heat tolerance) and the genetic correlation between farrowing rate and heat tolerance was estimated.Commercial production pigs are crossbreds farmed all over the world. In contrast, selection is practiced mainly in temperate climates, in nucleus herds using purebred pigs. The success of genetic selection depends on how much genetic progress is realized in crossbred pigs. Within this thesis these genetic correlations for farrowing rate between purebreds and crossbreds were estimated.

    Sow productivity depends on a number of related traits, such as ovulation rate, the number of litters per sow per year, the number of weaned piglets per sow per year, and the length of productive live. Traditionally pig breeding programs have improved sow productivity by increasing number weaned piglets per sow per year. To improve herd-level litters per sow per year a new trait was proposed called problem free sow production by parity, which incorporates the traits interval weaning first insemination, non-return rate, farrowing rate, and selection for next parity. Heritability of problem free sow production and genetic correlations with other sow production traits were estimated.

    The main conclusion of this thesis was that it is possible to select for improved heat resistance in addition to improved commercial production levels in commercial pigs. However, genetic correlation between production in temperate and hot climates is high. This high correlation implies that, within-line, pigs with the best performance in a hot climate will be the best in temperate climate too. Most important for the success of a pig breeding program is to define appropriate breeding goals which are based on the environment(s) that market pigs are expected to perform in. The overall data collection for the genetic evaluation needs to be done in those specific environments and this will favour pigs which are able to produce over more than one specific environment.

    Chemotaxis and oospore formation in Phytophthora sojae are controlled by G-protein-coupled receptors with a phosphatidylinositol phosphate kinase domain
    Yang, X. ; Zhao, W. ; Hua, C. ; Zheng, X. ; Jing, M. ; Li, D. ; Govers, F. ; Meijer, H.J.G. ; Wang, Y. - \ 2013
    Molecular Microbiology 88 (2013)2. - ISSN 0950-382X - p. 382 - 394.
    sexual reproduction - gene-expression - mating hormone - plasma-membrane - alpha-subunit - infestans - pathogen - oomycete - isoflavones - identification
    G-protein-coupled receptors (GPCRs) are key cellular components that mediate extracellular signals into intracellular responses. Genome mining revealed that Phytophthora spp. have over 60 GPCR genes among which a prominent class of 12 encoding novel proteins with an N-terminal GPCR domain fused to a C-terminal phosphatidylinositol phosphate kinase (PIPK) domain. This study focuses on two GPCR-PIPKs (GKs) in Phytophthora sojae. PsGK4 and PsGK5 are differentially expressed during the life cycle with the highest expression in cysts and during cyst germination, and at late infection stages. In P.¿sojae transformants that constitutively express RFP-tagged PsGK4 and PsGK5, the fusion proteins in hyphae reside in small, rapidly moving vesicular-like structures. Functional analysis using gene silencing showed that PsGK4-silenced transformants displayed higher levels of encystment and a reduced cyst germination rate when compared with the recipient strain. Moreover, GK4 deficiency (or reduction) resulted in severe defects in zoospore chemotaxis towards isoflavones and soybean roots. In contrast, PsGK5-silenced transformants exhibited no obvious defects in asexual development but oospore production was severely impaired. Both, PsGK4- and PsGK5-silenced transformants showed reduced pathogenicity. These results point to involvement of GKs in zoospore behaviour, chemotaxis and oospore development, and suggest that PsGK4 and PsGK5 each head independent signalling pathways.
    Reproduction in crabs: strategies, invasiveness and environmental influences thereon
    Brink, A.M. van den - \ 2013
    Wageningen University. Promotor(en): Han Lindeboom, co-promotor(en): Aad Smaal; C. McLay. - S.l. : s.n. - ISBN 9789461735232 - 164
    krabben (schaaldieren) - geslachtelijke voortplanting - geslachtsselectie - groei - voortplantingsvermogen - invasieve soorten - populatiedynamica - omgevingstemperatuur - milieufactoren - mariene ecologie - crabs - sexual reproduction - sexual selection - growth - reproductive performance - invasive species - population dynamics - environmental temperature - environmental factors - marine ecology

    This thesis provides insights into the interconnectedness of crab reproductive biology, the selective forces leading to their development, the possible links to invasiveness and the influences of environmental factors thereon. The empirical data collected and presented in this thesis can be used to compare different crab species and make predictions about the effect of climate change on their population dynamics and invasiveness.
    Two crab species in particular are examined in this thesis, Halicarcinus cookii and Hemigrapsus takanoi , which share similar size and habitat preferences, but have different reproductive strategies and statuses as endemic and invasive. The potential effects of increased water temperature due to climate change on the reproduction and eventual population changes in the species are investigated as well as the possible links reproduction and temperature have with the invasiveness of a species.
    Halicarcinus cookii is an endemic crab to the coasts of New Zealand and is not known anywhere else. The species shows determinate growth, hard shell mating, continuous brood production and ventral seminal receptacles. After the final moult the female produces numerous offspring limited only by sperm availability. With a hard shell the female also avoids mortality resulting from the regular vulnerable soft shell stage. Individuals mature over a range of sizes but do not continue growing after their pubertal moult. With such a terminal moult, brood size is limited by female size.

    Hemigrapsus takanoi is native to the north west Pacific, but has been introduced and is very successful in Europe. The species shows indeterminate growth, hard-shell mating, a defined breeding season and ventral seminal receptacles. With indeterminate growth they continue moulting and growing throughout their adult life. After their pubertal moult, these species can mate throughout the year and produce 2-3 broods between each moult. They are not limited in growth or regeneration of limbs and can safely hide from predators during the vulnerable soft-shell inter-moult period rather than mating which exposes them to predators.

    Despite their different reproductive strategies, broods of both species showed a similar reaction to increased water temperature in that the duration of development of the brood decreased as temperature increased. Extrapolating the results to a climate change scenario, it is suggested that with a temperature rise of 2°C H. cookii could produce one extra brood of over 1000 offspring per female life time, potentially leading to a 10-15% increase in fecundity and possible population growth. As H. takanoi does not show continuous brood production, predicting the effect of temperature rise is more difficult, but evidence suggests that fecundity is also likely to increase in this species with an increase in water temperature.

    Temperature increase may also lead to a change in invasiveness of a species. If areas currently below the optimum temperature for a species become warmer, it is possible that a species may spread to the new locations. Hemigrapsus takanoi may spread further north in Europe than it’s current distribution (assuming it is limited by temperature). Furthermore, if temperatures increase the rate of reproduction in a non-indigenous species, they may become more invasive in their present location.

    The colonisation of a new habitat will involve new interactions, such as predation and competition, with species not previously encountered. The interactions of the two invasive crab species H. takanoi and Hemigrapsus sanguineus with the native Carcinus maenas in the delta waters of SW Netherlands was also investigated in this thesis. Whereas C. maenas was the most common shore crab in these waters, its numbers have declined on the soft sediment substrates during the last 20 years. As the two invasive crab species were first recorded in the Dutch delta in 1999, they could not have initiated the decline of the native C. maenas. However, within a few years H. takanoi completely dominated the intertidal hard substrate environments; the same environments on which juvenile C. maenas depend. On soft sediment substrate the native and invasive crab species are presently more or less equally abundant. Nowadays H. takanoi appears to be a fierce interference competitor or predator for small C. maenas specimens by expelling them from their shelters. However, due to the habitat generalist nature of C. maenas, it is unlikely that the Hemigrapsus species will cause it’s local extinction. More likely is that they will learn to live together.

    The objective to provide new information about a rarely studied species (Halicarcinus cookii) was fulfilled in this thesis and the information can be used as bases for comparison for future research.

    The hypothesis that temperature has no effect on the reproductive rate of crabs was rejected as both study species showed similar increases in brood development rate with increased temperatures. This suggests that global temperature rises may increase the reproductive rate of wider crab populations.

    The hypothesis that the arrival, presence and effect of Hemigrapsus takanoi in the Dutch delta waters has had no effect on the native green crab Carcinus maenas was complicated by the fluctuations and the decrease in C. maenas numbers prior to the arrival of H. takanoi. It was concluded that while H. takanoi did not cause the initial decrease in the C. maenas population, it did take advantage of it and now dominates niches previously occupied by juvenile C. maenas where size dependent competition and/or predation on juvenile C. maenas occurs.

    Phytophthora infestans field isolates from Gansu Province, China are genetically highly diverse and show a high frequency of self fertility
    Han, M. ; Liu, G. ; Li, J.P. ; Govers, F. ; Zhu, X.Q. ; Shen, C.Y. ; Guo, L.Y. - \ 2013
    Journal of Eukaryotic Microbiology 60 (2013)1. - ISSN 1066-5234 - p. 79 - 88.
    mating hormone - sexual reproduction - populations - dna - netherlands - migrations
    The genetic diversity of 85 isolates of Phytophthora infestans collected in 2007 from Gansu province in China was determined and compared with 21 isolates collected before 2004. Among them, 70 belonged to the A1 mating type and 15 were self-fertile (SF). The mitochondrial DNA haplotypes revealed both Ia (25%) and IIa (75%) haplotypes. Metalaxyl resistance occurred with high frequency (54%) in Gansu. Simple sequence repeat (SSR) genotyping revealed 26 genotypes (13 from the Tianshui region) among the 85 isolates, and 18 genotypes among the 21 isolates collected before 2004, without overlap in genotypes detected in the two groups. Cluster analysis showed clear subdivisions within the different mating type isolates. Among Gansu's isolates, Nei's and Shannon's diversity indices were highest in isolates collected in Tianshui where both A1 and SF isolates were found. Analysis of molecular variance of isolates from Gansu indicated that 51% and 49% of the variance was explained by within-area and among-area variance, respectively. The results suggest that the occurrence of SF isolates increases the risk of sexual reproduction, the formation of oospore as initial inocula in the field, and affects the genotypic diversity in the population.
    Sexual selection in Fungi
    Nieuwenhuis, B.P.S. - \ 2012
    Wageningen University. Promotor(en): Rolf Hoekstra, co-promotor(en): Duur Aanen. - S.l. : s.n. - ISBN 9789461733580 - 156
    schimmels - geslachtsselectie - genetica - geslachtelijke voortplanting - evolutionaire genetica - evolutie - fungi - sexual selection - genetics - sexual reproduction - evolutionary genetics - evolution

    Sexual selection is an important factor that drives evolution, in which fitness is increased, not by increasing survival or viability, but by acquiring more or better mates. Sexual selection favours traits that increase the ability of an individual to obtain more matings than other individuals that it is in competition with. For many sexually reproducing organisms, obtaining mates is an essential part of the lifecycle, sexual selection can therefore be very strong. A trait that leads to more matings can be selected, even if it strongly reduces other components of fitness, for instance predator escape. Often sexual selection leads to sex specific traits, which can become very extravagant. In animals and plants, it has been well established that this form of selection is an important evolutionary force, but it has not been considered for fungi. This thesis revolves around the idea that in this aspect, fungi are not fundamentally different from animals and plants and that also for species from this kingdom sexual selection influences evolution. Many fungi reproduce sexually and need to find a partner before reproduction can proceed. Furthermore, it is likely that not all individuals that benefit from mating can perform mating, hence a struggle for mate acquisition will occur.
    In my research I have investigated how likely it is that in fungi such struggles occur and which mechanisms might act during competitions. For these studies I used the mushroom forming basidiomycete fungus Schizophyllum commune as a model organism. I studied the potential for mate competition in natural populations, performed laboratory mating essays to test competition and preference, and experimentally tested if sexual selection can increase competitive ability.
    Sexual reproduction in fungi is highly regulated. Many molecular mechanisms are known that modulate each step, from meiosis to gamete production and from mate finding to gamete fusion. In most fungi these characteristics are regulated by genes located on the mating type locus or loci. These genes do not only regulate mating, but also define compatibility between the gametes: gametes with the same alleles at a mating type locus cannot fuse. Because of this double function, fungal mating types are potentially very important for sexual selection. Besides that mating types are a target for sexual selection because they affect traits that might increase competitive ability, since the mating types determine compatibility, they also define who competes with whom. Sexual selection describes how within one sex mating occurs for individuals of the other sex and is therefore always intra-sexual. Fungi do not have different sexes, but do have sex roles. Sexual selection will therefore act if there is competition for mating in the male or female role. Compatibility between sex roles is different from compatibility between mating types. The first is defined by the size of the mycelium, and the second by a genetic recognition mechanism. This difference is of importance to understand how sexual selection can act in fungi and is explained in Chapter 2.
    Mating in mushroom fungi occurs by reciprocal exchange of nuclei. In the female role nuclei from a compatible mate are incorporated into the haploid mycelium. These nuclei migrate though the mycelium until in each cell of the mycelium two haploid nuclei are present; it becomes a so called dikaryon. Only a dikaryon can produce mushrooms that produce spores. In the male role, a mycelium can donate nuclei to a haploid mycelium. A mycelium can thus be considered hermaphroditic. After fertilize, the dikaryon can still act as a nucleus donor, but not incorporate more nuclei – this type of mating is known as the Buller phenomenon. Also spores can act as male, but as they have no mycelium, not as a female. Due to the presence of more individuals that can mate in the male role than there are female mycelia (monokaryons), competition over fertilizations is expected.
    Competition can only occur when there are multiple individuals. Fungi are sessile organisms that can only meet other individuals when they are in the same locality. To test whether there is potential for sexual selection in nature, the number of individuals that meet each other needs to be defined. Not much knowledge on numbers of individuals is known, because mushroom fungi generally grow by mycelium expansion inside a substratum and each part of the mycelium can produce mushrooms. Therefore, all mushrooms on a tree can be one genetic individual, but it is also possible that each mushroom is a separate individual. We sampled 24, 12 and 24 mushrooms from the same substrate of three natural populations to analyse how mating occurred (Chapter 3). We determined the identity of the two different nuclei in each mushroom, as well as the mitochondria. Because mitochondria do not migrate during mating, they are specific for each female mycelium. We found that multiple genetic individuals (3, 3 and 8) are present in a small area, and that many matings must have occurred. Even though it is generally assumed that matings occur between two monokaryons, none such matings were found. The data suggest that mating in nature occurs between a monokaryon and a spore, or a monokaryon and a dikaryon.
    During a dikaryon-monokaryon (di-mon) mating only one of the two nucleus types from the dikaryon is successful in fertilizing the monokaryon. The nucleus type that is successful will likely increase its fitness considerably, as the entire female mycelium becomes colonized. Sexual selection is expected to select for nuclei that are better in performing this fertilization. Furthermore, during mating the receiving monokaryon meets two different nuclei, and might be able to choose between them. We performed crosses between 15 dikaryons and six different monokaryons to test if selection occurs, and whether selection occurs by male-male competition, or by female choice (Chapter 4). When confronting the same dikaryon with different monokaryon, in some of the cases the female mycelium decided which of the two nuclei won. In most cases however, the same nucleus always fertilized the monokaryon, irrespective of which monokaryon. This suggests that nuclei are able to either manipulate the monokaryon in incorporating them into the mycelium and not the other type, or that the nuclei of one type can directly suppress mating by the other nuclei in the dikaryon.
    Nuclei in a dikaryon have a strict way of cell division in which the different types divide in synchrony. Probably the two nuclei keep each other in check to assure this synchrony. Experiments in which the two nuclei in a dikaryon are separated into monokaryons suggest that the two nuclei suppress each other’s mitotic division, and that one of the two nuclei is better in suppression than the other. Consequently, after de-dikaryotisation more monokaryons of one type are recovered than of the other. We tested if this mechanism of suppression might be responsible for the dominant nuclei in the di-mon matings (Chapter 5). Separating the two nuclei confirmed earlier findings that always one of the two nuclei is dominant and that a hierarchy in dominance exists. This pecking order did not correspond with the results from the winner in the di-mon matings, which suggests that the mechanism of suppressed mitotic division is not responsible for dominance in di-mon matings. Nevertheless, we argue that the hypothesis that a link between the two mechanisms exists should not be completely written off. Because the interactions that take place during di-mon matings are very complex, the functioning of this mechanism might be obscured during mating.
    The observed variance in mating success described above might lead to sexual selection, however, it does not show that sexual selection actually led to traits that improve increased mate acquisition. To show that traits can evolve that increase fitness by higher mating success, we performed an evolution experiment (Chapter 6). An evolving population of nuclei was continuously mated with a non-evolving monokaryon. This setup selected for novel traits that increase competitive ability over matings. After 20 transfers, four out of twelve evolved lines had increased in competitive fitness and one line had decreased. Different fitness components were measured to investigate which traits had resulted in changed fitness. Fertilization success was mainly determined at the moment of fusion with and in initial migration into the receiving monokaryon. Two strains showed increased spores production, but this did not add to the increased fitness caused by fusion and initial migration. Little fitness change occurred during migration or in the dikaryon phase. We observed no clear trade-offs between the competitive ability of fertilizing in the male role, and female characteristics. This experiment showed that sexual selection can act in mushroom fungi.
    Sexual selection can also play a role in other groups of fungi than the mushroom forming fungi. So far this has not been considered, and little research has been done to show how mate competition might influence evolution. We reinterpreted the current knowledge on mating in fungi and assessed whether and when sexual selection might play a role (Chapter 7). Sexual selection is most likely to occur when sex roles can be observed during mating, as this can lead to skewed sex ratios. Also when there is large difference in quality between potential mates sexual selection might lead to evolution of choice. Directions are given where sexual selection is expected to function in fungal mating. Examples are given of how sexual selection might have led to for instance the evolution of micro-conidia in ascomycetes and pheromone redundancy in basidiomycetes. Furthermore, the existence of different sex roles in fungi, can lead to sexual conflict between the genomes derived from the paternal and the maternal gametes of which examples are given. The realization that sexual selection can also act in fungi gives great opportunity to test how universal general theories of sexual selection are in another important group of organisms. Additionally, because fungi are easy to manipulate, predictions on sexual selection can be tested experimentally using fungi.
    Mushroom forming fungi have a life history which differs from animals and plants. Sexual selection will therefore affect mushroom fungi in a different manner than it would animals and plants. In the general discussion of this thesis (Chapter 8) I will assess how mating influences fungal fitness, teasing apart the benefits and costs of mating in the male and female roles. I give directions for future research and discuss a setup to directly measure the effect of pheromones on female choice in mushroom fungi.
    There are still many unanswered fundamental questions about sexual selection. Adding knowledge from a third important kingdom can help increase the understanding of the principles that drive evolution by sexual selection. Furthermore, applying sexual selection theory to fungi might elucidate the functioning of the sometimes very complex mechanisms that have evolved for fungal mating.

    The causes of epistasis
    Visser, J.A.G.M. de; Cooper, T.F. ; Elena, S.F. - \ 2011
    Proceedings of the Royal Society. B: Biological Sciences 278 (2011)1725. - ISSN 0962-8452 - p. 3617 - 3624.
    dna-bacteriophage phi-x174 - deleterious mutations - antibiotic-resistance - sexual reproduction - escherichia-coli - saccharomyces-cerevisiae - compensatory mutations - synergistic epistasis - beneficial mutations - digital organisms
    Since Bateson’s discovery that genes can suppress the phenotypic effects of other genes, gene interactions— called epistasis—have been the topic of a vast research effort. Systems and developmental biologists study epistasis to understand the genotype–phenotype map, whereas evolutionary biologists recognize the fundamental importance of epistasis for evolution. Depending on its form, epistasis may lead to divergence and speciation, provide evolutionary benefits to sex and affect the robustness and evolvability of organisms. That epistasis can itself be shaped by evolution has only recently been realized. Here, we review the empirical pattern of epistasis, and some of the factors that may affect the form and extent of epistasis. Based on their divergent consequences, we distinguish between interactions with or without mean effect, and those affecting the magnitude of fitness effects or their sign. Empirical work has begun to quantify epistasis in multiple dimensions in the context of metabolic and fitness landscape models.We discuss possible proximate causes (such as protein function and metabolic networks) and ultimate factors (including mutation, recombination, and the importance of natural selection and genetic drift). We conclude that, in general, pleiotropy is an important prerequisite for epistasis, and that epistasis may evolve as an adaptive or intrinsic consequence of changes in genetic robustness and evolvability
    Mitochondrial recombination increases with age in Podospora anserina
    Diepeningen, A.D. van; Goedbloed, D.J. ; Slakhorst, S.M. ; Koopmanschap-Memelink, A.B. ; Maas, M.F.P.M. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2010
    Mechanisms of Ageing and Development 131 (2010)5. - ISSN 0047-6374 - p. 315 - 322.
    group-ii introns - life-span - excision-amplification - sexual reproduction - sequence-analysis - plasmid pal2-1 - dna-sequence - wild-type - senescence - selection
    With uniparental inheritance of mitochondria, there seems little reason for homologous recombination in mitochondria, but the machinery for mitochondrial recombination is quite well-conserved in many eukaryote species. In fungi and yeasts heteroplasmons may be formed when strains fuse and transfer of organelles takes place, making it possible to study mitochondrial recombination when introduced mitochondria contain different markers. A survey of wild-type isolates from a local population of the filamentous fungus Podospora anserina for the presence of seven optional mitochondrial introns indicated that mitochondrial recombination does take place in nature. Moreover the recombination frequency appeared to be correlated with age: the more rapidly ageing fraction of the population had a significantly lower linkage disequilibrium indicating more recombination. Direct confrontation experiments with heterokaryon incompatible strains with different mitochondrial markers at different (relative) age confirmed that mitochondrial recombination increases with age. We propose that with increasing mitochondrial damage over time, mitochondrial recombination – even within a homoplasmic population of mitochondria – is a mechanism that may restore mitochondrial function
    Identifying hybridizing taxa within the Daphnia longispina species complex: a comparison of genetic methods and phenotypic approaches
    Dlouha, S. ; Thielsch, A. ; Kraus, R.H.S. ; Seda, J. ; Schwenk, K. ; Petrusek, S. - \ 2010
    Hydrobiologia 643 (2010)1. - ISSN 0018-8158 - p. 107 - 122.
    interspecific hybridization - cyclomorphic daphnia - sexual reproduction - concerted evolution - european daphnia - galeata complex - cladocera - crustacea - differentiation - mechanism
    Daphnia galeata Sars, D. longispina O. F. Muller and D. cucullata Sars (Crustacea: Cladocera) are closely related species which often produce interspecific hybrids in natural populations. Several marker systems are available for taxon determination in this hybridizing complex, but their performance and reliability has not been systematically assessed. We compared results from identifications by three molecular methods. More than 1,200 individuals from 10 localities in the Czech Republic were identified as parental species or hybrids by allozyme electrophoresis and the analysis of the restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP); over 440 of them were additionally analyzed and identified by 12 microsatellite loci. Identification by microsatellite markers corresponded well with allozyme analyses. However, consistent discrepancies between ITS-RFLP and other markers were observed in two out of 10 studied localities. Although some marker discrepancies may have been caused by occasional recent introgression, consistent deviations between ITS-RFLP and other markers suggest a long-term maintenance of introgressed alleles. These results warn against its use as a sole identification method in field studies. Additionally, we quantitatively evaluated the discriminatory power of geometric morphometric (elliptic Fourier) analysis of body shapes based on photos of over 1,300 individuals pre-classified by allozyme markers. Furthermore, a randomly selected subset of 240 individuals was independently determined from photos by several experts. Despite a tendency for morphological divergence among parental Daphnia species, some taxa (especially D. galeata, D. longispina, and their hybrids) substantially overlapped in their body shapes. This was reflected in different determination success for particular species and hybrids in discriminant analysis based on shape data as well as from photographs
    Taxonomy and phylogeny of the genus Mycosphaerella and its anamorphs
    Crous, P.W. - \ 2009
    Fungal Diversity 38 (2009). - ISSN 1560-2745 - p. 1 - 24.
    mating-type genes - leaf diseases - sexual reproduction - cercosporoid fungi - eucalyptus leaves - rdna sequence - ribosomal dna - south-africa - pathogen - teleomorph
    Historically plant pathogenic species of Mycosphaerella have been regarded as host-specific, though this hypothesys has proven difficult to test largely due to the inavailability of fungal cultures. During the course of the past 20 years a concerted effort has been made to collect these fungi, and devise methods to cultivate them. Based on subsequent DNA sequence analyses the majority of these species were revealed to be host-specific, though some were not, suggesting that no general rule can be applied. Furthermore, analysis of recent molecular data revealed Mycosphaerella to be poly- and paraphyletic. Teleomorph morphology was shown to be too narrowly defined in some cases, and again too widely in others. Mycosphaerella and Teratosphaeria as presently circumscribed represent numerous different genera, many of which can be recognised based on the morphology of their 30 odd associated anamorph genera. Although Mycosphaerella is generally accepted to represent one of the largest genera of ascomycetous fungi, these data suggest that this is incorrect, and that Mycosphaerella should be restricted to taxa linked to Ramularia anamorphs. Furthermore, other anamorph form genera with Mycosphaerella-like teleomorphs appear to represent genera in their own right.
    Evolution of plant reproduction: from fusion and dispersal to interaction and communication
    Willemse, M.T.M. - \ 2009
    Chinese Science Bulletin 54 (2009)14. - ISSN 1001-6538 - p. 2390 - 2403.
    sexual reproduction - mechanisms
    Based on the existing data concerning the evolution of the sexual reproduction, it is argued that the processes of sex differentiation and interactions play a key role in evolution. From the beginning environment and organism are unified. In a changing dynamic environment life originates and the interaction between life and environment develops from simple to more complex organisms. Sexual reproduction is introduced after the origin of meiosis and is a key process in evolution. The asexual reproduction process prepares to dispersal. Sexual reproduction process adds the genome renewal and the gamete-gamete interaction. Reproduction and dispersal are connected and the process of reproduction has similarities between asexual and sexual reproduction. Unicellular algae develop the physiological and morphological sex differentiation. Sex differentiation is connected with the way of dispersal. The step to multicellular plants introduces cell isolation after meiosis and by the stay on the mother plant within a cell or organ, plant-cell apoplastic interaction originates and by prolonged stay the plant-plant interaction. This stay influences the type of dispersal. A life cycle with alternation of generations and two moments of dispersal permits plants to go on land. In ferns a shift in the moment of sex differentiation to meiospore happens and the stay of the macrospore leads to the seed plants. In water all types of sexual reproduction, interactions and the alternation of generations are prepared and these are used to conquest land. On land the biotic dispersal is realized. The phylogeny of sexual reproduction reveals that the sex differentiation and interaction are the main causes in the evolution of sexual reproduction. Sexual reproduction shows interactions during gamete fusion, between organism and environment and in multicellular plants between organisms. With respect to other types of interaction as in symbiosis or the nutrient chain, interaction is considered as an important action which is based on a persisting cooperation and points to a push during evolution. The push is expressed as communication: the driving force in the evolution. Based on the interactions between organisms and interactions between organisms and the dynamic environment, communication is considered as a driving force leading to the evolution as explained in the development of plant reproduction. Consequences for reproduction, its regulation and the process of evolution are discussed
    Population size and habitat quality affect genetic diversity and fitness in the clonal herb Cirsium dissectum
    Vere, N. de; Jongejans, E. ; Plowman, A. ; Williams, E. - \ 2009
    Oecologia 159 (2009)1. - ISSN 0029-8549 - p. 59 - 68.
    sexual reproduction - plant conservation - paris-quadrifolia - fen-meadow - management - pratensis - establishment - performance - environment - extinction
    Remaining populations of plant species in fragmented landscapes are threatened by declining habitat quality and reduced genetic diversity, but the interactions of these major factors are rarely studied together for species conservation. In this study, the interactions between population size, habitat quality, genetic diversity and fitness were investigated in 22 populations of the clonal herb Cirsium dissectum throughout the British Isles. Regression analysis was used to identify significant factors, and a structural equation model was developed to illustrate and integrate these interactions. It was found that smaller populations (measured as the total number of plants) had lower genetic diversity (proportion of polymorphic loci), and that reduced genetic diversity (allelic richness) had a negative impact on the survival of seedlings grown under standard conditions. Habitat quality also had a large effect on C. dissectum. Unmanaged sites with tall vegetation, no bare soil and higher nutrient levels had smaller populations of C. dissectum, but flowering was promoted. Flowering was suppressed in heavily grazed sites with short vegetation. Higher levels of bare soil and phosphorus both had a positive relationship with genetic diversity, but probably for distinctly different reasons: bare soil provides safe sites for establishment, whilst phosphorus may promote flowering and improve seed germination. In order to conserve C. dissectum, management needs to maintain site heterogeneity so that C. dissectum can flower and establishment gaps are still available for seedlings; when either component is reduced, negative feedbacks through reduced genetic diversity and individual fitness can be expected. This study therefore highlights the importance of considering both conservation genetics and habitat quality in the conservation of plant species
    Demographic vulnerability of the clonal and endangered meadow thistle
    Jongejans, E. ; Vere, N. de; Kroon, H. de - \ 2008
    Plant Ecology 198 (2008)2. - ISSN 1385-0237 - p. 225 - 240.
    population viability analysis - extinction risk - sexual reproduction - biological flora - perennial herb - british-isles - plants - dynamics - grassland - fragmentation
    For effective management of endangered species it is pivotal to understand why a species is endangered and which key life cycle components are involved in its response to environmental changes. Our objective was to investigate the response of rosettes of the redlisted clonal herb Cirsium dissectum to anthropogenic nutrient enrichment, which threatens its populations, and the consequences of these responses for its population dynamics. We constructed matrix population models with demographic data from three populations and four annual transitions and we decomposed the spatiotemporal variation in projected population growth rates into contributions from life cycle components. These patterns were compared with below-ground rosette dynamics in different fields, and with the below- and above-ground rosette dynamics in a garden experiment with nutrient enrichment and competing grasses. The decomposition analysis revealed that increased clonal rosette formation and decreased rosette survival were driving the spatial variation in the population growth rate. Excavating the below-ground rhizome network revealed a higher rosette turn-over in experimentally fertilized garden plots, which not only resulted in increased plot-level extinction, but also in increased spread of the clonal offspring. This supported the observed trend among field populations: rosette formation trades off with rosette survival. Surviving seedlings were only found in areas where the topsoil had been removed. The endangered C. dissectum is vulnerable when its habitat becomes more productive, because this species does not have the necessary capability to build up biomass. Small-scale disturbances such as created by sod-cutting or trampling cattle are essential for seedling establishment and necessary to render the explorative strategy of rhizomatous clonal spread successful.
    Discovery of a functional Mycosphaerella teleomorph in the presumed asexual barley pathogen Septoria passerinii
    Ware, S.B. ; Verstappen, E.C.P. ; Breeden, J. ; Cavaletto, J.R. ; Goodwin, S.B. ; Waalwijk, C. ; Crous, P.W. ; Kema, G.H.J. - \ 2007
    Fungal Genetics and Biology 44 (2007)5. - ISSN 1087-1845 - p. 389 - 397.
    mating-type idiomorphs - cryptococcus-neoformans - rhynchosporium-secalis - fusarium-oxysporum - leaf blotch - graminicola pathosystem - sexual reproduction - genetic-variation - tritici blotch - host cultivars
    We studied the possibility of a teleomorph associated with the genotypically diverse septoria speckled leaf blotch (SSLB) pathogen of barley, Septoria passerinii. A teleomorph in the genus Mycosphaerella had been predicted previously based on phylogenetic analyses. This prediction was tested with experiments in the Netherlands and the United States by co-inoculating isolates with opposite mating types onto susceptible barley cultivars and monitoring leaves for sexual structures and for the discharge of ascospores. Characterization of putative hybrid progeny by both molecular (AFLP, RAPD, mating type, and ITS sequencing) and phenotypic analyses confirmed that a Mycosphaerella teleomorph of S. passerinii has been discovered approximately 125 years after the description of the anamorph. Progeny had recombinant genotypes of the molecular alleles present in the parents, and the identities of representative progeny isolates as S. passerinii were confirmed by ITS sequencing. A previously unknown sexual cycle explains the high degree of genetic variation among isolates found in nature. The experimental identification of a predicted teleomorph for S. passerinii indicates that cryptic sexual cycles may be common for many other ¿asexual¿ fungi with high levels of genotypic diversity.
    Aspects of sexual reproduction in Mycosphaerella species on wheat and barley : genetic studies on specificity, mapping, and fungicide resistance
    Ware, S.B. - \ 2006
    Wageningen University. Promotor(en): Pierre de Wit, co-promotor(en): Gert Kema; M.A. de Waard. - [S.l.] : S.n. - ISBN 9789085045274 - 190
    triticum aestivum - tarwe - hordeum vulgare - gerst - mycosphaerella graminicola - geslachtelijke voortplanting - plantenziekteverwekkende schimmels - septoria - gastheerspecificiteit - genetische kartering - resistentie tegen pesticiden - virulentie - pathogeniteit - ziekteresistentie - overleving - triticum aestivum - wheat - hordeum vulgare - barley - mycosphaerella graminicola - septoria - sexual reproduction - survival - plant pathogenic fungi - host specificity - virulence - pathogenicity - genetic mapping - pesticide resistance - disease resistance

    Mycosphaerella species are haploid ascomycetes that cause major economic losses in crops that include cereals, citrus fruits, and bananas, among others. Two organisms in this genus are Mycosphaerella graminicola (Fuckel) .I. Schröt (anamorph Sepioria tritici) and Septoriapasserinii. M graminicola is the causal agent of septoria tritici blotch of both bread wheat and durum wheat species, and S. passerinii causes septoria speck!ed 1eaf blotch of barley. M. graminicola is a heterothaliic fungus with a very active sexual cycle, while no sexual cycle has been reported for S. passerinii.

    This thesis inciudes studies on mating and genetics of both M. graminicola and S. passerinii. Chapter 1 gives an introduction to these pathogens and an overview of the research topics. In Chapter 2. we studied the possibility of in planta generation of sexual progeny of the fungal wheat pathogen M graminicola when one of the parents was avirulent on a resistant host. We found that avirulent isolates are able to survive and even increase in biomass after inoculation onto resistant wheat cultivars and can complete sexual cycles on resistant cultivars to yield viable ascospores as long as the other parent is virulent. To our knowledge, this is the first time such a phenomenon has been described, and the possibility to generate such crosses opened the door for studies in Chapters 3 and 4.

    Chapter 3 describes the construction of two high-density genetic linkage maps of M graminicola using Diversity Arrays Technology (DArT) and the integration of these into a core map with common markers due to a common parental isolate. One of the maps was constructed based on segregations of progeny of two bread wheat-derived isolates, IPO323 and IPO94269, and the other was constructed from segregations of progeny of IPO323 and the durum wheat-derived isolate IPO95052. In total, 1,144 markers made up the integrated core map. Analyses from this study revealed that progeny had translocations, diploid and partial diploid linkage groups, and loss of entire linkage groups.

    Although M. graminicola causes disease on both bread wheat and durum wheat, isolates within the population show clear distinctions in either virulence on bread wheat or on durum wheat (host specificity)- In Chapter 4, we studied the genetic basis of host specificity in M. graminicola using 163 progeny from crosses between the Dutch bread wheat-derived 1PO323 and the Algerian durum wheat-derived TPO95052. Phenotyping of progeny was performed on a set of seven differential cultivars, and progeny crossed on either bread wheat or durum wheat could infect cultivars of bread wheat, durum wheat, both, or neither. These results were used to map nine quantitative trait loci (QTLs) on seven linkage groups in the high-densiry genetic linkage map from Chapter 3. One of these loci was previously mapped for cultivar specificity of IPO323in bread wheat, and the same locus was now mapped for host specificity of IPO323 to durum wheat. Our results show that the reported host specificity is probably the result of combinations of a number of independently inherited avirulence factors.

    In addition to avirulence genes, fungi can inherit other traits for survival. One such heritable trait is a point mutation in the mitochondrial genome that conveys resistance to strobilurin fungicides. Chapter 5 describes a study on the inheritance of strobilurin resistance. Resistant and sensitive isolates of M. graminicola were crossed on wheat seedlings that were both untreated and preventively treated with various concentrations of azoxystrobin (Amistar™), and progeny were analyzed to determine the rate of inheritance of the aforementioned mutation. Preventive rates from 3.125-200% Amistar™ resulted in completely resistant progeny populations despite the fact that the segregation of nuclear genes confirmed regular meiotic behavior. We conclude that sensitive isolates overcome the disruption of mitochondrial respiration and participate in sexual reproduction even under high fungicide pressure and that fungicide stress induces or results in preferential mating in M. graminicola.

    The barley pathogen S. passerinii clusters closely to M. graminicola in phylogenetic studies based on ITS sequences, and a high degree of genetic variation among isolates is found in nature. However, no teleomorph has been reported for this S. passerinii, and hence, it was considered to be asexual. Nevertheless, mating type idiomorphs were recently detected and isolated. In Chapter 6, we studied the possibility of a Mycosphaerella teleomorph associated with S. passerinii. Isolates with opposite mating types were co-inoculated onto barley cultivars, and leaves were monitored for the discharge of ascospores. Characterization of a segregating population by both molecular and phenotypic analyses confirmed that we successfully generated the hitherto unknown Mycosphaerella teleomorph of S. passerinii.

    Finally, the results of this thesis are discussed in a broader perspective in Chapter 7 in relation to epidemiology, co-evolution, and durability of resistance in the wheat-M. graminicola pathosystem. The proven ability of avirulent isolates of M. graminicola to generate sexual progeny on resistant cultivars represents a new dynamic in population genetics that has not'previously been considered in epidemiology. Resu!ts from this thesis emphasize the complex ways in which the sexual cycle contributes to the overall success of M. graminicola on wheat.

    The interplay between shifts in biomass allocation and costs of reproduction in four grassland perennials under simulated successional change
    Jongejans, E. ; Kroon, H. de; Berendse, F. - \ 2006
    Oecologia 147 (2006)2. - ISSN 0029-8549 - p. 369 - 378.
    resource-allocation - nutrient availability - sexual reproduction - population-dynamics - species-diversity - clonal plant - competition - vegetation - heathland - growth
    When perennial herbs face the risk of being outcompeted in the course of succession, they are hypothesized to either increase their biomass allocation to flowers and seeds or to invest more in vegetative growth. We tested these hypotheses in a 3-year garden experiment with four perennials (Hypochaeris radicata, Cirsium dissectum, Succisa pratensis and Centaurea jacea) by growing them in the midst of a tall tussock-forming grass (Molinia caerulea) that may successionally replace them in their natural habitat. In all species except for the short-lived H. radicata, costs of sexual reproduction were significant over the 3 years, since continuous bud removal enhanced total biomass or rosette number. To mimic succession we added nutrients, which resulted in a tripled grass biomass and higher death rates in the shorter-lived species. The simulated succession resulted also in a number of coupled growth responses in the survivors: enhanced plant size as well as elevated seed production. The latter was partly due to larger plant sizes, but mostly due to higher reproductive allocation, which in turn could be partly explained by lower relative somatic costs and by lower root¿shoot ratios in the high-nutrient plots. Our results suggest that perennial plants can increase both their persistence and their colonization ability by simultaneously increasing their vegetative size and reproductive allocation in response to enhanced competition and nutrient influxes. These responses can be very important for the survival of a species in a metapopulation context.
    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.
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