114 results on '"Kraaijeveld K"'
Search Results
2. Evidence for involvement of a transformer paralogue in sex determination of the wasp Leptopilina clavipes
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Geuverink, E., Kraaijeveld, K., Leussen, M. van, Chen, F., Pijpe, J., Linskens, M.H.K., Beukeboom, L.W., Zande, L. van de, and Animal Ecology
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transformer-2 ,reproductive modes ,Hymenoptera ,protein interactions ,transformer orthologue - Abstract
Transformer (tra) is the central gear in many insect sex determination pathways and transduces a wide range of primary signals. Mediated by transformer-2 (tra2) it directs sexual development into the female or male mode. Duplications of tra have been detected in numerous Hymenoptera, but a function in sex determination has been confirmed only in Apis mellifera. We identified a tra2 orthologue (Lc-tra2), a tra orthologue (Lc-tra) and a tra paralogue (Lc-traB) in the genome of Leptopilina clavipes (Hymenoptera: Cynipidae). We compared the sequence and structural conservation of these genes between sexual (arrhenotokous) and asexual all-female producing (thelytokous) individuals. Lc-tra is sex-specifically spliced in adults consistent with its orthologous function. The male-specific regions of Lc-tra are conserved in both reproductive modes. The paralogue Lc-traB lacks the genomic region coding for male-specific exons and can only be translated into a full-length TRA-like peptide sequence. Furthermore, unlike LC-TRA, the LC-TRAB interstrain sequence variation is not differentiated into a sexual and an asexual haplotype. The LC-TRAB protein interacts with LC-TRA as well as LC-TRA2. This suggests that Lc-traB functions as a conserved element in sex determination of sexual and asexual individuals.
- Published
- 2018
3. Insecten als wijnmakers
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Joanna Sundstrom, Jennie Gardner, Whiteside, M. D., Kraaijeveld, K., Kiers, E. T., Jacintha Ellers, Vladimir Jiranek, and Animal Ecology
- Published
- 2016
4. Evidence for involvement of atransformerparalogue in sex determination of the waspLeptopilina clavipes
- Author
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Geuverink, E., primary, Kraaijeveld, K., additional, van Leussen, M., additional, Chen, F., additional, Pijpe, J., additional, Linskens, M. H. K., additional, Beukeboom, L. W., additional, and van de Zande, L., additional
- Published
- 2018
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5. Granulocyte colony-stimulating factor enhances protection by anti-K1 capsular IgM antibody in murine Escherichia coli sepsis
- Author
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HUSTINX, W., BENAISSA-TROUW, B., VAN KESSEL, K., KUENEN, J., TAVARES, L., KRAAIJEVELD, K., VERHOEF, J., and HOEPELMAN, A.
- Published
- 1997
6. A new case of Wolbachia dependence in the genus Asobara: evidence for parthenogenesis induction in Asobara japonica
- Author
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Kremer, N., Charif, D., Henri, H., Bataile, M., Prevost, G., Kraaijeveld, K., and Vavre, F.
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Parthenogenesis -- Research ,Wolbachia -- Genetic aspects ,Cladistic analysis -- Usage ,Arthropoda -- Genetic aspects ,Arthropoda -- Sexual behavior ,Host-bacteria relationships -- Research ,Biological sciences - Published
- 2009
7. Peer Review #1 of "Penetrance of symbiont-mediated parthenogenesis is driven by reproductive rate in a parasitoid wasp (v0.1)"
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Kraaijeveld, K, additional
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- 2017
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8. Transposon proliferation in an asexual parasitoid
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Kraaijeveld, K., Zwanenburg, B., Hubert, B., Vieira, C., Pater, S. de, Alphen, J.J.M. van, Dunnen, J.T. den, Knijff, P. de, Institute Biology Leiden (IBL), Universiteit Leiden [Leiden], Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), Universiteit Leiden, and Universiteit Leiden-Universiteit Leiden
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asexual reproduction ,[SDV]Life Sciences [q-bio] ,next-generation sequencing ,transposable elements ,Wolbachia - Abstract
International audience; The widespread occurrence of sex is one of the most elusive problems in evolutionary biology. Theory predicts that asexual lineages can be driven to extinction by uncontrolled proliferation of vertically transmitted transposable elements (TEs), which accumulate because of the inefficiency of purifying selection in the absence of sex and recombination. To test this prediction, we compared genome-wide TE load between a sexual lineage of the parasitoid wasp Leptopilina clavipes and a lineage of the same species that is rendered asexual by Wolbachia-induced parthenogenesis. We obtained draft genome sequences at 15-20× coverage of both the sexual and the asexual lineages using next-generation sequencing. We identified transposons of most major classes in both lineages. Quantification of TE abundance using coverage depth showed that copy numbers in the asexual lineage exceeded those in the sexual lineage for DNA transposons, but not LTR and LINE-like elements. However, one or a small number of gypsy-like LTR elements exhibited a fourfold higher coverage in the asexual lineage. Quantitative PCR showed that high loads of this gypsy-like TE were characteristic for 11 genetically distinct asexual wasp lineages when compared to sexual lineages. We found no evidence for an overall increase in copy number for all TE types in asexuals as predicted by theory. Instead, we suggest that the expansions of specific TEs are best explained as side effects of (epi)genetic manipulations of the host genome by Wolbachia. Asexuality is achieved in a myriad of ways in nature, many of which could similarly result in TE proliferation.
- Published
- 2012
9. Clonal genetic variation in a Wolbachia-infected asexual wasp: horizontal transmission or historical sex?
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Kraaijeveld, K., Franco, P., Knijff, P. de, Stouthamer, R., and Alphen, J.J.M. van
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phylogeography ,bacteria ,host parasite interactions ,evolution of sex - Published
- 2011
10. Metabolic rate affects adult life span independently of developmental rate in parasitoid wasps
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Seyahooei, M.A., van Alphen, J.J.M., Kraaijeveld, K., and Population Biology (IBED, FNWI)
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fungi - Abstract
Developmental time and body size correlate with lifespan in a wide range of taxa, although not in insect parasitoids. When the rate of development is independent of adult metabolic rate, adult lifespan is free to adapt to the adult environment. We suggest that interspecific variation in intrinsic adult metabolic rates, differences in allocation of lipids to longevity, and reproduction and differences in the ability to use carbohydrates as an adult should all result in variation of adult lifespan, independent of development time. To test these ideas, we measured metabolic rate, lipid content and egg load at eclosion, developmental time, and lifespan of females with and without carbohydrate food in five species of Asobara, which represent parasitoids of Drosophila. No relationship between development time and adult longevity was found. As predicted, metabolic rates varied between species and appeared to trade off with adult longevity. We found no clear link between initial egg load and the longevity of a species, suggesting that lipid allocation may be less important in determining adult lifespan. The results obtained indicate that differences in metabolic rate have an important effect on adult lifespan, without affecting developmental rate in parasitoids.
- Published
- 2011
11. Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life
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Faddeeva, A., primary, Studer, R. A., additional, Kraaijeveld, K., additional, Sie, D., additional, Ylstra, B., additional, Mariën, J., additional, op den Camp, H. J. M., additional, Datema, E., additional, den Dunnen, J. T., additional, van Straalen, N. M., additional, and Roelofs, D., additional
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- 2015
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12. Goed en kwaad op het witte doek
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Hoorn, J.F., Konijn, E.A., Kraaijeveld, K., Literature, Language, Literature and Communication, and Art and Culture, History, Antiquity
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- 2000
13. Why Seychelles Warblers fail to recolonize nearby islands: Unwilling or unable to fly there?
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Komdeur, J., Piersma, T., Kraaijeveld, K., Kraaijeveld-Smit, F., Richardson, David S., Komdeur lab, and Piersma group
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BIRDS ,PHYLOGENY ,BASAL METABOLIC-RATE ,FLIGHTLESSNESS ,INSECTS ,CALIDRIS-CANUTUS ,MORPHOLOGY ,EVOLUTION - Abstract
The Seychelles Warbler Acrocephalus sechellensis is a rare island endemic which, from 1920 to 1988, occurred only on Cousin Island (29 ha) in the Seychelles. Despite the saturated nature of this population and the possibility of obtaining higher reproductive success on new nearby islands, inter-island dispersal by Seychelles Warblers is extremely rare (0.10%). We test the hypothesis that Seychelles Warblers show an adaptation typical for island birds: a low-cost reduced-size flight apparatus. We compared the anatomy of the flight apparatus (wing shape, wing loading, skeletal parts and musculature) of Seychelles Warblers with that of three closely related migratory Acrocephalus species (Eurasian Reed Warbler A. scirpaceus, Australian Reed Warbler A. australis and African Reed Warbler A. baeticatus). Seychelles Warblers do not differ from the migratory warblers in pectoral mass and skeletal attachment area relative to body mass, wing shape and wing loading. Seychelles Warblers show the morphological structures required for sustained flight, but may have the behavioural reluctance to cross what they may regard as extensive bodies of water.
- Published
- 2004
14. Synthetic polysaccharide type 3-related di-, tri-, and tetrasaccharide-CRM197 conjugates induce protection against Streptococcus pneumoniae type 3 in mice
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Vliegenthart, J.F.G., Benaissa-Trouw, B., Lefeber, D.J., Kamerling, J.P., Kraaijeveld, K., and Snippe, H.
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Scheikunde - Abstract
Di-, tri-, and tetrasaccharides, synthesized according to the chemical structure of pneumococcal polysaccharide type 3 (PS3), were coupled to the cross-reactive material (CRM197) of modified diphtheria toxin in different molar carbohydrate/protein ratios using the squarate coupling method. To study protective immunity, female BALB/c mice were subcutaneously immunized twice (with a 3-week interval) using the amount of conjugates corresponding to 2.5 µg of oligosaccharide per mouse. The conjugates evoked PS3 binding immunoglobulin G antibodies that lasted for at least 7 weeks after the booster. Immunogenicity was not influenced by the carbohydrate/protein ratio. All mice with PS3-specific antibodies survived the intraperitoneal challenge with Streptococcus pneumoniae type 3. Therefore, synthetic oligosaccharide-protein conjugates might have potential as vaccines.
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- 2001
15. Occasional males in parthenogenetic populations of Asobara japonica (Hymenoptera: Braconidae): low Wolbachia titer or incomplete coadaptation?
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Reumer, B M, primary, van Alphen, J J M, additional, and Kraaijeveld, K, additional
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- 2011
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16. Mating system, philopatry and patterns of kinship in the cooperatively breeding subdesert mesiteMonias benschi
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SEDDON, N., primary, AMOS, W., additional, ADCOCK, G., additional, JOHNSON, P., additional, KRAAIJEVELD, K., additional, KRAAIJEVELD‐SMIT, F. J. L., additional, LEE, W., additional, SENAPATHI, G. D., additional, MULDER, R. A., additional, and TOBIAS, J. A., additional
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- 2005
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17. Mutual ornamentation, sexual selection, and social dominance in the black swan
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Kraaijeveld, K., primary
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- 2004
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18. Extra-pair paternity does not result in differential sexual selection in the mutually ornamented black swan (Cygnus atratus)
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Kraaijeveld, K., primary, Carew, P. J., additional, Billing, T., additional, Adcock, Greg J., additional, and Mulder, Raoul A., additional
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- 2004
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19. Evaluation of protection by two endotoxin-neutralizing IgM monoclonal antibodies in different peritonitis models
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Hustinx, W. N., primary, Benaissa-Trouw, B. J., additional, Harmsen, T., additional, Klein, S., additional, Verhoef, J., additional, Hoepelman, A. I., additional, and Kraaijeveld, K., additional
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- 1997
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20. Cross-protection by anti-core glycolipid antibodies: evidence from animal experiments
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Hustinx, W. N., primary, Kraaijeveld, K., additional, Hoepelman, A. I., additional, and Verhoef, J., additional
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- 1997
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21. Effect of imipenem on monoclonal antibody-mediated protection against Escherichia coli O18K5
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Frasa, H, primary, Benaissa-Trouw, B, additional, Tavares, L, additional, van Kessel, K, additional, Hustinx, W, additional, Schellekens, J, additional, Kraaijeveld, K, additional, and Verhoef, J, additional
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- 1996
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22. Enhanced protection by use of a combination of anticapsule and antilipopolysaccharide monoclonal antibodies against lethal Escherichia coli O18K5 infection of mice
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Frasa, H, primary, Benaissa-Trouw, B, additional, Tavares, L, additional, van Kessel, K, additional, Poppelier, M, additional, Kraaijeveld, K, additional, and Verhoef, J, additional
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- 1996
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23. Escherichia coli in bacteremia: O-acetylated K1 strains appear to be more virulent than non-O-acetylated K1 strains
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Frasa, H, primary, Procee, J, additional, Torensma, R, additional, Verbruggen, A, additional, Algra, A, additional, Rozenberg-Arska, M, additional, Kraaijeveld, K, additional, and Verhoef, J, additional
- Published
- 1993
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24. Occasional males in parthenogenetic populations of Asobara japonica (Hymenoptera: Braconidae): low Wolbachia titer or incomplete coadaptation?
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Reumer, B M, van Alphen, J J M, and Kraaijeveld, K
- Subjects
HYMENOPTERA ,BRACONIDAE ,PARASITOIDS ,WOLBACHIA ,NUCLEOTIDE sequence - Abstract
Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. Some populations of the parasitoid wasp Asobara japonica are infected with Wolbachia and reproduce parthenogenetically, while other populations are not infected and reproduce sexually. Wolbachia-infected A. japonica females regularly produce small numbers of male offspring. Because all females in the field are infected and infected females are not capable of sexual reproduction, male production seems to be maladaptive. We investigated why these females nevertheless produce males. We tested three hypotheses: high rearing temperatures could result in higher offspring sex ratios (more males), low Wolbachia titer of the mother could lead to higher offspring sex ratios and/or the Wolbachia infection is of relatively recent origin and not enough time has passed to allow complete coadaptation between Wolbachia and host. In all, 33% of the Wolbachia-infected females produced males and 56% of these males were also infected with Wolbachia. Neither offspring sex ratio nor male infection frequency was significantly affected by rearing temperature or Wolbachia concentration of the mother. The mitochondrial DNA sequence of one of the uninfected populations was identical to that of two of the infected populations. Therefore, the initial Wolbachia infection of A. japonica must have occurred recently. Mitochondrial sequence variation among the infected populations suggests that the spread of Wolbachia through the host populations involved horizontal transmission. We conclude that the occasional male production by Wolbachia-infected females is most likely a maladaptive side effect of incomplete coevolution between symbiont and host in this relatively young infection. [ABSTRACT FROM AUTHOR]
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- 2012
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25. Mating system, philopatry and patterns of kinship in the cooperatively breeding subdesert mesite Monias benschi.
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Seddon, N., Amos, W., Adcock, G., Johnson, P., Kraaijeveld, K., Kraaijeveld-Smit, F. J. L., Lee, W., Senapathi, G. D., Mulder, R. A., and Tobias, J. A.
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COOPERATIVE breeding in animals ,ANIMAL sexual behavior ,FAMILIAL behavior in animals ,ANIMAL behavior ,MOLECULAR ecology ,MOLECULAR biology - Abstract
In the first molecular study of a member of the threatened avian family, Mesitornithidae, we used nine polymorphic microsatellite loci to elucidate parentage, patterns of within-group kinship and occurrence of extra-group paternity in the subdesert mesite Monias benschi, of southwest Madagascar. We found this cooperatively breeding species to have a very fluid mating system. There was evidence of genetic monogamy and polygynandry: of the nine groups with multiple offspring, six contained one breeding pair with unrelated helpers and three contained multiple male and female breeders with related helpers. Although patterns of within-group kinship varied, there was a strong positive relationship between group size and relatedness, suggesting that groups form by natal philopatry. There was also a strong positive correlation between within-sex and between-sex relatedness, indicating that unlike most cooperatively breeding birds, philopatry involved both sexes. In contrast to predictions of kin selection and reproductive skew models, all monogamous groups contained unrelated individuals, while two of the three polygynandrous groups were families. Moreover, although between-group variation in seasonal reproductive success was related to within-group female relatedness, relatedness among males and between the sexes had no bearing on a group's reproductive output. While kin selection may underlie helping behaviour in females, factors such as direct long-term fitness benefits of group living probably determine helping in males. Of the 14 offspring produced by fully sampled groups, at least two were sired by males from neighbouring groups: one by a breeding male and one by a nonbreeding male, suggesting that males may augment their reproductive success through extra-group paternity. [ABSTRACT FROM AUTHOR]
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- 2005
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26. In vivo TNF induction by culture supernatants of antibiotic-treated Escherichia coli 07:K1. Role of antibiotic class and concentration
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Hustinx, W. N. M., Benaissa-Trouw, B. J., Tweel, I. Van der, Harmsen, T., Verhoef, J., Hoepelman, A. I. M., and Kraaijeveld, K. A.
- Published
- 1996
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27. Genetic structure of Leptopilina boulardi populations from different climatic zones of Iran
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van Alphen Jacques JM, Seyahooei Majeed, and Kraaijeveld Ken
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Ecology ,QH540-549.5 - Abstract
Abstract Background The genetic structure of populations can be influenced by geographic isolation (including physical distance) and ecology. We examined these effects in Leptopilina boulardi, a parasitoid of Drosophila of African origin and widely distributed over temperate and (sub) tropical climates. Results We sampled 11 populations of L. boulardi from five climatic zones in Iran and measured genetic differentiation at nuclear (Amplified Fragment Length Polymorphism; AFLP) and mitochondrial (Cytochrome Oxidase I; COI) loci. An Analysis of Molecular Variance (AMOVA) for the AFLP data revealed that 67.45% of variation resided between populations. No significant variation was observed between climatic zones. However, a significant difference was detected between populations from the central (dry) regions and those from the wetter north, which are separated by desert. A similarly clear cut genetic differentiation between populations from the central part of Iran and those from the north was observed by UPGMA cluster analysis and Principal Coordinates Analysis (PCO). Both UPGMA and PCO further separated two populations from the very humid western Caspian Sea coast (zone 3) from other northern populations from the temperate Caspian Sea coastal plain (zone 2), which are connected by forest. One population (Nour) was genetically intermediate between these two zones, indicating some gene flow between these two groups of populations. In all analyses a mountain population, Sorkhabad was found to be genetically identical to those from the nearby coastal plain (zone 2), which indicates high gene flow between these populations over a short geographical distance. One population from the Caspian coast (Astaneh) was genetically highly diverged from all other populations. A partial Mantel test showed a highly significant positive correlation between genetic and geographic distances, as well as separation by the deserts of central Iran. The COI sequences were highly conserved among all populations. Conclusion The Iranian populations of L. boulardi showed clear genetic structure in AFLP profiles, but not in COI sequence data. The transfer of fruits containing Drosophila larvae parasitized by L. boulardi appears to have caused some unexpected gene flow and changed the genetic composition of populations, particularly in urban areas. Nevertheless, our results suggest that climate, geographic distance and physical barriers may all have contributed to the formation of genetically distinct populations of L. boulardi. Inevitably, there will be overlap between the portions of variance explained by these variables. Disentangling the relative contributions of climate and geography to the genetic structure of this species will require additional sampling.
- Published
- 2011
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28. The evolutionary loss of lipogenesis in insect parasitoids: Molecular mechanisms and ecological aspects
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Lammers, M., Ellers, J, Kraaijeveld, K., and Animal Ecology
- Published
- 2020
29. Co-evolution between parthenogenesis-inducing Wolbachia and its hosts
- Author
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Reumer, B.M., Alphen, J.J.M. van, Kraaijeveld, K., and Leiden University
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fungi ,Parthenogenesis ,Life history traits ,biochemical phenomena, metabolism, and nutrition ,Mitochondrial DNA ,Sexual functionality ,Tetrastichus coeruleus ,Sexual vs. asexual populations ,parasitic diseases ,bacteria ,Microsatellites ,Sex ratio ,reproductive and urinary physiology ,Wolbachia ,Asobara japonica - Abstract
Wolbachia are intracellular, symbiotic bacteria, known for their ability to manipulate the reproduction mechanism of their arthropod hosts, for example by inducing parthenogenesis. In this thesis, I studied the causes, consequences and dynamics of a parthenogenesis-inducing (PI) Wolbachia infection in two hosts, the parasitoid wasps Tetrastichus coeruleus (Hymenoptera: Eulophidae) and Asobara japonica (Hymenoptera: Braconidae). Interestingly, both T. coeruleus and A. japonica have Wolbachia-infected parthenogenetic populations and uninfected sexual populations. The main conclusions of this thesis are as follows. First, different scenarios may occur for the spread of PI-Wolbachia infection in different host species. Wolbachia has spread via vertical transmission through populations of T. coeruleus, whereas in A. japonica Wolbachia has spread via horizontal transmission. Second, different barriers may prevent migration and gene flow between Wolbachia-infected and uninfected populations in different host species. In T. coeruleus the different populations occur in different ecological environments, whereas in A. japonica there seems to be a geographical barrier between the different populations. Third, different ages of the PI-Wolbachia infection may have different consequences for the host species. The occasional male production by Wolbachia-infected A. japonica might be explained by the relatively young age of the infection. The Wolbachia infection in T. coeruleus seems to be older. Last, a PI-Wolbachia infection can have severe consequences for the sexual functionality of infected males and females. PI-Wolbachia seems to induce cytoplasmic incompatibility in infected A. japonica males. PI-Wolbachia-infected T. coeruleus females exhibited a degradation of receptivity to matings and of spermathecal morphology.
- Published
- 2012
30. Life-history evolution in hymenopteran parasitoids : the roles of host and climate
- Author
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Seyahooei, M.A., Alphen, J.J.M. van, Kraaijeveld, K., Brakefield, P.M., Ellers, J., Kinkaamer, P., Dooren, T. van, and Leiden University
- Subjects
Egg size ,Host ,Climate ,fungi ,Egg load ,Life-history ,Metabolic rate ,Parasitoid - Abstract
In this thesis I studied the relationships between parasitoids, hosts and climate from an evolutionary point of view by using hymenopteran parasitoids as a model system. A comparative approach was used to study the variation in life-history traits of species or populations from different habitats. I showed that closely related species manipulate their host behaviour differently and allocate their essential resources to different life-history traits during development. Metabolic rate and energy reserves varied strongly between species. At the population level, energy reserves were found differ substantially between different climate zones. A molecular study revealed clear genetic divergence of these populations, which partially reflected the pattern in life-history variation. To conclude, I suggest that life-history traits of parasitoids are subject to natural selection pressures from both host and cli mate. Resource allocation and host manipulation in parasitoids is species specific and highly diverged among populations to fit habitat requirements.
- Published
- 2010
31. ONT read assembly of the black rhino genome.
- Author
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Kraaijeveld K, Bossers K, Petrusevski N, Pieterman S, Bruins-van Sonsbeek LGR, and Wittink F
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- Male, Animals, Perissodactyla genetics, Persistent Infection, Research Design, Genetic Research, Nose
- Abstract
Objectives: The black rhinoceros (Diceros bicornis) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo's often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced and assembled the genome of a captive male black rhino using ONT sequencing data only., Data Description: This work produced over 100 Gb whole genome sequencing reads from whole blood. These were assembled into a 2.47 Gb draft genome consisting of 834 contigs with an N50 of 29.53 Mb. The genome annotation was lifted over from an available genome annotation for black rhino, which resulted in the retrieval of over 99% of gene features. This new genome assembly will be a valuable resource in for conservation genetic research in this species., (© 2024. The Author(s).)
- Published
- 2024
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32. On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes.
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van der Gulik PTS, Egas M, Kraaijeveld K, Dombrowski N, Groot AT, Spang A, Hoff WD, and Gallie J
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- RNA, Transfer genetics, Genome
- Abstract
Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the mis-categorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, non-canonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions.
- Published
- 2023
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33. Towards evolutionary predictions: Current promises and challenges.
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Wortel MT, Agashe D, Bailey SF, Bank C, Bisschop K, Blankers T, Cairns J, Colizzi ES, Cusseddu D, Desai MM, van Dijk B, Egas M, Ellers J, Groot AT, Heckel DG, Johnson ML, Kraaijeveld K, Krug J, Laan L, Lässig M, Lind PA, Meijer J, Noble LM, Okasha S, Rainey PB, Rozen DE, Shitut S, Tans SJ, Tenaillon O, Teotónio H, de Visser JAGM, Visser ME, Vroomans RMA, Werner GDA, Wertheim B, and Pennings PS
- Abstract
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions., Competing Interests: The authors declare that there is no conflict of interest., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)
- Published
- 2022
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34. Adult size and timing of reproduction in five species of Asobara parasitoid wasps.
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Askari Seyahooei M, Kraaijeveld K, Bagheri A, and van Alphen JJM
- Subjects
- Animals, Body Size, Female, Reproduction, Species Specificity, Time Factors, Wasps growth & development, Wasps physiology
- Abstract
The majority of adult parasitoid wasps are unable to synthesize lipids and therefore face a trade-off between the investment of lipids in eggs or in the maintenance of soma. It has been shown that resource allocation should depend on body size in parasitoids. Given that smaller females have shorter expected life times, they should concentrate their reproductive effort into early life. To test this prediction, we investigated the relationship between body size and the timing of egg production in parasitoids. We measured body size, lipid reserves, and reproductive investment (number of eggs, ovigeny index equivalent [OIE] and egg size) at eclosion in five species of Asobara (Hymenoptera: Braconidae) originating from different geographic and climatic environments. Our results show significant interspecific variation in all these traits. A diagnostic test for phylogenetic independence revealed that closely related species did not resemble each other more closely than expected by chance for all traits measured. Lipid reserves scaled positively with body size both between and within species. In agreement with theory, OI correlated negatively with body size both between and within species. Total egg area at eclosion correlated negatively with lipid reserves both between and within species. This indicates the existence of a trade-off between allocation of lipids to current reproduction and survival/future reproduction. With the exception of the most extreme pro-ovigenic species, A. persimilis, we found that pro-ovigeny was compensated for by small egg size. Our results indicate the role of habitats in shaping interspecific variation in resource allocation strategies., (© 2019 Institute of Zoology, Chinese Academy of Sciences.)
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- 2020
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35. Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.
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Roelofs D, Zwaenepoel A, Sistermans T, Nap J, Kampfraath AA, Van de Peer Y, Ellers J, and Kraaijeveld K
- Subjects
- Animals, Arthropods genetics, Phylogeny, Evolution, Molecular, Gene Duplication, Genome, Insecta genetics
- Abstract
Background: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals., Results: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (K
S ), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs., Conclusions: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.- Published
- 2020
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36. The Importance of Validating the Demethylating Effect of 5-aza-2'-deoxycytidine in Model Species (A Comment on Cook et al., "DNA Methylation and Sex Allocation in the Parasitoid Wasp Nasonia vitripennis ").
- Author
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Ellers J, Visser M, Mariën J, Kraaijeveld K, and Lammers M
- Subjects
- Animals, Azacitidine, Decitabine, Sex Ratio, DNA Methylation, Wasps
- Abstract
The use of DNA demethylating agents has been popular in epigenetic studies. Recently, Cook and colleagues, in a 2015 American Naturalist article, claimed an effect of 5-aza-2'-deoxycytidine (5-aza-dC) on the sex ratio of a parasitoid wasp without verifying its effect on DNA methylation. We repeated the 5-aza-dC feeding treatment to test its effectiveness. We used bisulfite amplicon sequencing of 10 genes that either were heavily methylated, previously showed a response to 5-aza-dC, or were suggested to regulate fatty acid synthesis epigenetically, and we demonstrate that wasps fed 5-aza-dC did not show reduced DNA methylation at these loci. Therefore, the conclusion that demethylation shifts sex ratios upward needs reconsideration.
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- 2019
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37. The genome of the live-bearing fish Heterandria formosa implicates a role of conserved vertebrate genes in the evolution of placental fish.
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van Kruistum H, van den Heuvel J, Travis J, Kraaijeveld K, Zwaan BJ, Groenen MAM, Megens HJ, and Pollux BJA
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- Animals, Female, Gene Duplication, Pregnancy, Selection, Genetic, Whole Genome Sequencing, Biological Evolution, Conserved Sequence, Cyprinodontiformes genetics, Genome, Placenta physiology
- Abstract
Background: The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ's complexity by a tiny amount. This evolutionary process can be studied by comparing closely related species that vary in the presence or absence of their organs. This is the case for the placenta in the live-bearing fish family Poeciliidae, as members of this family vary markedly in their ability to supply nutrients to their offspring via a placenta. Here, we investigate the genomic basis underlying this phenotypic variation in Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes may have played a role in the evolution of the placenta in the Poeciliidae., Results: We sequenced the genome of H. formosa, providing the first whole genome sequence for a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. Using comparative evolutionary analyses, we found 17 genes that were positively selected exclusively in H. formosa, as well as five gene duplications exclusive to H. formosa. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation., Conclusions: Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.
- Published
- 2019
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38. Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids.
- Author
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Lammers M, Kraaijeveld K, Mariën J, and Ellers J
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- Animals, Drosophila melanogaster genetics, Drosophila melanogaster metabolism, Genetic Pleiotropy, Transcription, Genetic, Wasps physiology, Evolution, Molecular, Lipogenesis genetics, Wasps genetics, Wasps metabolism
- Abstract
Background: Trait loss is a pervasive phenomenon in evolution, yet the underlying molecular causes have been identified in only a handful of cases. Most of these cases involve loss-of-function mutations in one or more trait-specific genes. However, in parasitoid insects the evolutionary loss of a metabolic trait is not associated with gene decay. Parasitoids have lost the ability to convert dietary sugars into fatty acids. Earlier research suggests that lack of lipogenesis in the parasitoid wasp Nasonia vitripennis is caused by changes in gene regulation., Results: We compared transcriptomic responses to sugar-feeding in the non-lipogenic parasitoid species Nasonia vitripennis and the lipogenic Drosophila melanogaster. Both species adjusted their metabolism within 4 hours after sugar-feeding, but there were sharp differences between the expression profiles of the two species, especially in the carbohydrate and lipid metabolic pathways. Several genes coding for key enzymes in acetyl-CoA metabolism, such as malonyl-CoA decarboxylase (mcd) and HMG-CoA synthase (hmgs) differed in expression between the two species. Their combined action likely blocks lipogenesis in the parasitoid species. Network-based analysis showed connectivity of genes to be negatively correlated to the fold change of gene expression. Furthermore, genes involved in the fatty acid metabolic pathway were more connected than the set of genes of all metabolic pathways combined., Conclusion: High connectivity of lipogenesis genes is indicative of pleiotropic effects and could explain the absence of gene degradation. We conclude that modification of expression levels of only a few little-connected genes, such as mcd, is sufficient to enable complete loss of lipogenesis in N. vitripennis.
- Published
- 2019
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39. Genomic Resources for Goniozus legneri , Aleochara bilineata and Paykullia maculata , Representing Three Independent Origins of the Parasitoid Lifestyle in Insects.
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Kraaijeveld K, Neleman P, Mariën J, de Meijer E, and Ellers J
- Subjects
- Animals, Behavior, Animal, Biological Evolution, Evolution, Molecular, Molecular Sequence Annotation, Phylogeny, Whole Genome Sequencing, Coleoptera genetics, Diptera genetics, Genome, Insect, Hymenoptera genetics
- Abstract
Parasitoid insects are important model systems for a multitude of biological research topics and widely used as biological control agents against insect pests. While the parasitoid lifestyle has evolved numerous times in different insect groups, research has focused almost exclusively on Hymenoptera from the Parasitica clade. The genomes of several members of this group have been sequenced, but no genomic resources are available from any of the other, independent evolutionary origins of the parasitoid lifestyle. Our aim here was to develop genomic resources for three parasitoid insects outside the Parasitica. We present draft genome assemblies for Goniozus legneri , a parasitoid Hymenopteran more closely related to the non-parasitoid wasps and bees than to the Parasitica wasps, the Coleopteran parasitoid Aleochara bilineata and the Dipteran parasitoid Paykullia maculata The genome assemblies are fragmented, but complete in terms of gene content. We also provide preliminary structural annotations. We anticipate that these genomic resources will be valuable for testing the generality of findings obtained from Parasitica wasps in future comparative studies., (Copyright © 2019 Kraaijeveld et al.)
- Published
- 2019
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40. No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods.
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Brandt A, Bast J, Scheu S, Meusemann K, Donath A, Schütte K, Machida R, and Kraaijeveld K
- Subjects
- Animals, Evolution, Molecular, Insecta classification, Selection, Genetic, Silent Mutation, Species Specificity, Conserved Sequence, Insecta genetics, Mutation Accumulation, Reproduction, Asexual genetics
- Abstract
Loss of sex and recombination is generally assumed to impede the effectiveness of purifying selection and to result in the accumulation of slightly deleterious mutations. Empirical evidence for this has come from several studies investigating mutational load in a small number of individual genes. However, recent whole transcriptome based studies have yielded inconsistent results, hence questioning the validity of the assumption of mutational meltdown in asexual populations. Here, we study the effectiveness of purifying selection in eight asexual hexapod lineages and their sexual relatives, as present in the 1 K Insect Transcriptome Evolution (1KITE) project, covering eight hexapod groups. We analyse the accumulation of slightly deleterious nonsynonymous and synonymous point mutations in 99 single copy orthologue protein-coding loci shared among the investigated taxa. While accumulation rates of nonsynonymous mutations differed between genes and hexapod groups, we found no effect of reproductive mode on the effectiveness of purifying selection acting at nonsynonymous and synonymous sites. Although the setup of this study does not fully rule out nondetection of subtle effects, our data does not support the established consensus of asexual lineages undergoing 'mutational meltdown'.
- Published
- 2019
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41. Regulatory and sequence evolution in response to selection for improved associative learning ability in Nasonia vitripennis.
- Author
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Kraaijeveld K, Oostra V, Liefting M, Wertheim B, de Meijer E, and Ellers J
- Subjects
- Alleles, Animals, Base Sequence, Drosophila melanogaster genetics, Gene Expression Regulation, Gene Regulatory Networks, Genetic Variation, Genome, Insect, Open Reading Frames genetics, Polymorphism, Single Nucleotide genetics, Sequence Analysis, DNA, Evolution, Molecular, Learning, Regulatory Sequences, Nucleic Acid genetics, Selection, Genetic, Wasps genetics
- Abstract
Background: Selection acts on the phenotype, yet only the genotype is inherited. While both the phenotypic and genotypic response to short-term selection can be measured, the link between these is a major unsolved problem in evolutionary biology, in particular for complex behavioural phenotypes., Results: Here we characterize the genomic and the transcriptomic basis of associative learning ability in the parasitic wasp Nasonia vitripennis and use gene network analysis to link the two. We artificially selected for improved associative learning ability in four independent pairs of lines and identified signatures of selection across the genome. Allele frequency diverged consistently between the selected and control lines in 118 single nucleotide polymorphisms (SNPs), clustering in 51 distinct genomic regions containing 128 genes. The majority of SNPs were found in regulatory regions, suggesting a potential role for gene expression evolution. We therefore sequenced the transcriptomes of selected and control lines and identified 36 consistently differentially expressed transcripts with large changes in expression. None of the differentially expressed genes also showed sequence divergence as a result of selection. Instead, gene network analysis showed many of the genes with consistent allele frequency differences and all of the differentially expressed genes to cluster in a single co-expression network. At a functional level, both genomic and transcriptomic analyses implicated members of gene networks known to be involved in neural plasticity and cognitive processes., Conclusions: Taken together, our results reveal how specific cognitive abilities can readily respond to selection via a complex interplay between regulatory and sequence evolution.
- Published
- 2018
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42. Evidence for involvement of a transformer paralogue in sex determination of the wasp Leptopilina clavipes.
- Author
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Geuverink E, Kraaijeveld K, van Leussen M, Chen F, Pijpe J, Linskens MHK, Beukeboom LW, and van de Zande L
- Subjects
- Alternative Splicing, Amino Acid Sequence, Animals, Base Sequence, Conserved Sequence, Evolution, Molecular, Female, Male, Ploidies, Insect Proteins physiology, Parthenogenesis, Sex Determination Processes, Wasps physiology
- Abstract
Transformer (tra) is the central gear in many insect sex determination pathways and transduces a wide range of primary signals. Mediated by transformer-2 (tra2) it directs sexual development into the female or male mode. Duplications of tra have been detected in numerous Hymenoptera, but a function in sex determination has been confirmed only in Apis mellifera. We identified a tra2 orthologue (Lc-tra2), a tra orthologue (Lc-tra) and a tra paralogue (Lc-traB) in the genome of Leptopilina clavipes (Hymenoptera: Cynipidae). We compared the sequence and structural conservation of these genes between sexual (arrhenotokous) and asexual all-female producing (thelytokous) individuals. Lc-tra is sex-specifically spliced in adults consistent with its orthologous function. The male-specific regions of Lc-tra are conserved in both reproductive modes. The paralogue Lc-traB lacks the genomic region coding for male-specific exons and can only be translated into a full-length TRA-like peptide sequence. Furthermore, unlike LC-TRA, the LC-TRAB interstrain sequence variation is not differentiated into a sexual and an asexual haplotype. The LC-TRAB protein interacts with LC-TRA as well as LC-TRA2. This suggests that Lc-traB functions as a conserved element in sex determination of sexual and asexual individuals., (© 2018 The Authors. Insect Molecular Biology published by John Wiley & Sons Ltd on behalf of Royal Entomological Society.)
- Published
- 2018
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43. Defensive repertoire of Drosophila larvae in response to toxic fungi.
- Author
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Trienens M, Kraaijeveld K, and Wertheim B
- Subjects
- Animals, Aspergillus nidulans, Drosophila melanogaster microbiology, Genes, Insect, Larva genetics, Larva microbiology, Transcriptome, Drosophila melanogaster genetics, Host-Pathogen Interactions genetics
- Abstract
Chemical warfare including insecticidal secondary metabolites is a well-known strategy for environmental microbes to monopolize a food source. Insects in turn have evolved behavioural and physiological defences to eradicate or neutralize the harmful microorganisms. We studied the defensive repertoire of insects in this interference competition by combining behavioural and developmental assays with whole-transcriptome time-series analysis. Confrontation with the toxic filamentous fungus Aspergillus nidulans severely reduced the survival of Drosophila melanogaster larvae. Nonetheless, the larvae did not behaviourally avoid the fungus, but aggregated at it. Confrontation with fungi strongly affected larval gene expression, including many genes involved in detoxification (e.g., CYP, GST and UGT genes) and the formation of the insect cuticle (e.g., Tweedle genes). The most strongly upregulated genes were several members of the insect-specific gene family Osiris, and CHK-kinase-like domains were over-represented. Immune responses were not activated, reflecting the competitive rather than pathogenic nature of the antagonistic interaction. While internal microbes are widely acknowledged as important, our study emphasizes the underappreciated role of environmental microbes as fierce competitors., (© 2017 John Wiley & Sons Ltd.)
- Published
- 2017
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44. Candidate genes for shell colour polymorphism in Cepaea nemoralis .
- Author
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Kerkvliet J, de Boer T, Schilthuizen M, and Kraaijeveld K
- Abstract
The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell's nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism., Competing Interests: The authors declare there are no competing interests.
- Published
- 2017
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45. Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.
- Author
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Faddeeva-Vakhrusheva A, Kraaijeveld K, Derks MFL, Anvar SY, Agamennone V, Suring W, Kampfraath AA, Ellers J, Le Ngoc G, van Gestel CAM, Mariën J, Smit S, van Straalen NM, and Roelofs D
- Subjects
- Animals, Anti-Bacterial Agents biosynthesis, Arthropods metabolism, Gene Rearrangement, Gene Transfer, Horizontal, Multigene Family genetics, Phylogeny, Arthropods genetics, Arthropods physiology, Genomics, Soil
- Abstract
Background: Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle., Results: We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster., Conclusions: The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.
- Published
- 2017
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46. Inter- and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack.
- Author
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Salazar-Jaramillo L, Jalvingh KM, de Haan A, Kraaijeveld K, Buermans H, and Wertheim B
- Subjects
- Animals, Evolution, Molecular, Genes, Insect genetics, Molecular Sequence Annotation, Sequence Homology, Nucleic Acid, Species Specificity, Drosophila genetics, Drosophila parasitology, Gene Expression Profiling, Genomics, Host-Parasite Interactions, Wasps physiology
- Abstract
Background: Parasitoid resistance in Drosophila varies considerably, among and within species. An immune response, lamellocyte-mediated encapsulation, evolved in a subclade of Drosophila and was subsequently lost in at least one species within this subclade. While the mechanisms of resistance are fairly well documented in D. melanogaster, much less is known for closely related species. Here, we studied the inter- and intra-species variation in gene expression after parasitoid attack in Drosophila. We used RNA-seq after parasitization of four closely related Drosophila species of the melanogaster subgroup and replicated lines of D. melanogaster experimentally selected for increased resistance to gain insights into short- and long-term evolutionary changes., Results: We found a core set of genes that are consistently up-regulated after parasitoid attack in the species and lines tested, regardless of their level of resistance. Another set of genes showed no up-regulation or expression in D. sechellia, the species unable to raise an immune response against parasitoids. This set consists largely of genes that are lineage-restricted to the melanogaster subgroup. Artificially selected lines did not show significant differences in gene expression with respect to non-selected lines in their responses to parasitoid attack, but several genes showed differential exon usage., Conclusions: We showed substantial similarities, but also notable differences, in the transcriptional responses to parasitoid attack among four closely related Drosophila species. In contrast, within D. melanogaster, the responses were remarkably similar. We confirmed that in the short-term, selection does not act on a pre-activation of the immune response. Instead it may target alternative mechanisms such as differential exon usage. In the long-term, we found support for the hypothesis that the ability to immunologically resist parasitoid attack is contingent on new genes that are restricted to the melanogaster subgroup.
- Published
- 2017
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47. Genome Sequencing of the Behavior Manipulating Virus LbFV Reveals a Possible New Virus Family.
- Author
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Lepetit D, Gillet B, Hughes S, Kraaijeveld K, and Varaldi J
- Subjects
- Animals, DNA Viruses physiology, Drosophila virology, Evolution, Molecular, Genes, Viral, Genome, Viral, Host-Parasite Interactions, Insect Viruses physiology, Phylogeny, Polymorphism, Single Nucleotide, Viral Proteins genetics, DNA Viruses genetics, Drosophila parasitology, Insect Viruses genetics, Wasps virology
- Abstract
Parasites are sometimes able to manipulate the behavior of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to being maternally transmitted, the virus benefits from horizontal transmission in superparasitized larvae (Drosophila that have been parasitized several times). Interestingly, the virus forces infected females to lay eggs in already parasitized larvae, thus increasing the chance of being horizontally transmitted. In a first step towards the identification of virus genes responsible for the behavioral manipulation, we present here the genome sequence of the virus, called LbFV. The sequencing revealed that its genome contains an homologous repeat sequence (hrs) found in eight regions in the genome. The presence of this hrs may explain the genomic plasticity that we observed for this genome. The genome of LbFV encodes 108 ORFs, most of them having no homologs in public databases. The virus is however related to Hytrosaviridae, although distantly. LbFV may thus represent a member of a new virus family. Several genes of LbFV were captured from eukaryotes, including two anti-apoptotic genes. More surprisingly, we found that LbFV captured from an ancestral wasp a protein with a Jumonji domain. This gene was afterwards duplicated in the virus genome. We hypothesized that this gene may be involved in manipulating the expression of wasp genes, and possibly in manipulating its behavior.
- Published
- 2016
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48. Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp.
- Author
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Kraaijeveld K, Anvar SY, Frank J, Schmitz A, Bast J, Wilbrandt J, Petersen M, Ziesmann T, Niehuis O, de Knijff P, den Dunnen JT, and Ellers J
- Subjects
- Animals, Female, Male, Mutation, Phenotype, Phylogeny, Polymorphism, Single Nucleotide, Wasps physiology, Genes, Insect, Reproduction, Asexual, Wasps genetics
- Abstract
Trait loss is a widespread phenomenon with pervasive consequences for a species’ evolutionary potential. The genetic changes underlying trait loss have only been clarified in a small number of cases. None of these studies can identify whether the loss of the trait under study was a result of neutral mutation accumulation or negative selection. This distinction is relatively clear-cut in the loss of sexual traits in asexual organisms. Male-specific sexual traits are not expressed and can only decay through neutral mutations, whereas female-specific traits are expressed and subject to negative selection. We present the genome of an asexual parasitoid wasp and compare it to that of a sexual lineage of the same species. We identify a short-list of 16 genes for which the asexual lineage carries deleterious SNP or indel variants, whereas the sexual lineage does not. Using tissue-specific expression data from other insects, we show that fifteen of these are expressed in male-specific reproductive tissues. Only one deleterious variant was found that is expressed in the female-specific spermathecae, a trait that is heavily degraded and thought to be under negative selection in L. clavipes. Although the phenotypic decay of male-specific sexual traits in asexuals is generally slow compared with the decay of female-specific sexual traits, we show that male-specific traits do indeed accumulate deleterious mutations as expected by theory. Our results provide an excellent starting point for detailed study of the genomics of neutral and selected trait decay.
- Published
- 2016
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49. No Accumulation of Transposable Elements in Asexual Arthropods.
- Author
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Bast J, Schaefer I, Schwander T, Maraun M, Scheu S, and Kraaijeveld K
- Subjects
- Animals, Genome, Genomics, Arthropods genetics, DNA Transposable Elements, Evolution, Molecular, Reproduction, Asexual genetics
- Abstract
Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads., (© The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2016
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50. Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects.
- Author
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Vrijenhoek T, Kraaijeveld K, Elferink M, de Ligt J, Kranendonk E, Santen G, Nijman IJ, Butler D, Claes G, Costessi A, Dorlijn W, van Eyndhoven W, Halley DJ, van den Hout MC, van Hove S, Johansson LF, Jongbloed JD, Kamps R, Kockx CE, de Koning B, Kriek M, Lekanne Dit Deprez R, Lunstroo H, Mannens M, Mook OR, Nelen M, Ploem C, Rijnen M, Saris JJ, Sinke R, Sistermans E, van Slegtenhorst M, Sleutels F, van der Stoep N, van Tienhoven M, Vermaat M, Vogel M, Waisfisz Q, Marjan Weiss J, van den Wijngaard A, van Workum W, Ijntema H, van der Zwaag B, van IJcken WF, den Dunnen J, Veltman JA, Hennekam R, and Cuppen E
- Subjects
- Calcium-Binding Proteins genetics, Cardiac Myosins genetics, Cardiomyopathies genetics, Carrier Proteins genetics, Exome, Gene Expression, High-Throughput Nucleotide Sequencing instrumentation, High-Throughput Nucleotide Sequencing methods, Humans, Informed Consent legislation & jurisprudence, Laboratory Proficiency Testing statistics & numerical data, MAP Kinase Kinase Kinases genetics, Myosin Heavy Chains genetics, Netherlands, Protein Serine-Threonine Kinases, Cardiomyopathies diagnosis, Genetic Testing standards, Genome, Human, High-Throughput Nucleotide Sequencing standards, Mutation
- Abstract
Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care.
- Published
- 2015
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