Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    A comparison of microsatellites and SNPs in parental assignment in the GIFT strain of Nile tilapia (Oreochromis niloticus): The power of exclusion
    Trong, T.Q. ; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Dibbits, B.W. ; Komen, J. - \ 2013
    Aquaculture 388-391 (2013). - ISSN 0044-8486 - p. 14 - 23.
    genotyping errors - computer-program - empirical-evaluation - natural-populations - markers - wild - inference - paternity - sibship - salmon
    In this study, parental assignment was studied in the 10th generation of a pedigreed selected Nile tilapia (Oreochromis niloticus) population (GIFT) and their offspring, by comparing two types of molecular markers, microsatellites and SNPs, using an exclusion-based (Vitassign) and a likelihood-based (Cervus) method. For the experiment, G10 parents were divided in 4 groups (cohorts) and allowed to produce offspring by natural group mating. In total 173 offspring were tested against 238 parents, using either 12 microsatellites (PIC = 0.639; exclusion power 68.0%) or 122 SNPs (PIC = 0.341; exclusion power 99.9%). In this study, more than half of the candidate parents were either full- or half-sibs with other parents. Furthermore, 13.8% of the parents died before being sampled for DNA. When offspring were assigned to parents in the same cohort, using Vitassign, for microsatellites, allowing up to 2 mismatches, 37.6% offspring got unique assignments, 45.1% got multiple assignments, and 17.3% were not assigned; for SNPs with up to 15 mismatches allowed, 83.8% offspring got unique assignments while 13.9% got multiple assignments. Only 2.3% were not assigned. Using Cervus, for microsatellites, the mean ‘strict’ (> 95% CF) assignment rate across the 4 cohorts was 18%, the ‘relax’ (80–95% CF) assignment rate was 43%, and 39% were not assigned; for SNPs, 39% ‘strict’ assignments were obtained (mean across 4 cohorts); the remaining offspring were not assigned. In general assignment rates were higher when cohort offspring were assigned to all parents combined, irrespective of method (Vitassign or Cervus) or marker used. However, consistency of assignments between microsatellites and SNPs was low: 28% with Vitassign and 16% with Cervus. Consistency of assignments between Cervus and Vitassign was high with SNPs (65%), but was low with microsatellites (31%). We conclude that missing parents and relatedness among candidate parents resulted in low assignment rates. Furthermore, low exclusion power of the microsatellite set resulted in low assignment rates and multiple parent pair assignments irrespective of method used. Exclusion methods and likelihood-based methods can be equally good for parental assignments, providing that good marker sets with high exclusion power are available.
    Mating, hybridisation and introgression in Lasius ants
    Have, T.M. van der; Pedersen, J.S. ; Boomsma, J.J. - \ 2011
    Myrmecological News 15 (2011). - ISSN 1994-4136 - p. 109 - 115.
    nuptial flights - niger - paternity - populations - evolution - ecology - alienus - fauna
    Recent reviews have shown that hybridisation among ant species is likely to be more common than previously appreciated. but that documented cases of introgression remain rare. After molecular phylogenetic work had shown that European Lasius niger (LINNAEUS, 1758) and L. psammophilus SEIFERT, 1992 (formerly L. alienus (FOERSTER. 1850)) are unlikely to be very closely related, we decided to analyse an old data set confirming the conclusion by PEARSON (1983) that these two ants can indeed form viable hybrids. We show that signatures of introgression can be detected in a Danish site and that interspecific gene-flow is asymmetrical (only from L. niger into L. psammophilus) as inferred previously by Pearson for the southern England site that he studied and from which we also collected data. We compare the observed patterns of hybridisation and introgression in the Danish and British site and infer that overlap in nuptial flights in Denmark may have contributed to the higher frequency of introgressed genes relative to the southern England site where nuptial flights are clearly separated in time. We also report the first mating system data for L. psammophilus. showing that this species has facultative multiple mating of queens similar to L. niger. We suggest that L. psammoplillus-niger introgression may be much more common than previously appreciated, which would explain that European myrmecologists have often found it difficult to distinguish between these species at sites where they occur sympatrically. This would imply that multiple accessible field sites are available to study the molecular details of hybridisation and introgression between two ant species that have variable degrees of sympatiy throughout their distributional ranges
    Is only the first mating effective for females in the Kanzawa spider mite, Tetranychus kanzawai (Acari: Tetranychidae)?
    Oku, K. - \ 2008
    Experimental and Applied Acarology 45 (2008)1-2. - ISSN 0168-8162 - p. 53 - 57.
    sperm competition - urticae acari - paternity - behavior
    Although only the first mating is effective for females in Tetranychus urticae (Acari: Tetranychidae), it remains unclear whether this is also true for closely related species, such as T. kanzawai. To address this question, I analyzed paternity in the progeny of T. kanzawai females that had been observed to copulate with two males by using a microsatellite DNA marker. In this study, mating was allowed to take place without experimental interruption. The results show that progenies were sired by both males in only 1 of 14 families, whereas progeny were sired only by the first males in the other families. This result suggests that only the first mating would be, by and large, effective in T. kanzawai.
    Hoog percentage achtergrondbestuivingen in eikenzaadgaard in Nederland
    Buiteveld, J. ; Bovenschen, J. ; Vries, S.M.G. de - \ 2003
    Nederlands Bosbouwtijdschrift (2003)3. - ISSN 0028-2057 - p. 24 - 28.
    bosbomen - quercus robur - zaden - zaadproductie - zaadbronnen - zaadbomen - zaadtuinen - zaadkwaliteit - bestuiving - bevruchting - vaderschap - vaders - afstamming - dna - genetische merkers - genetische verontreiniging - genetische analyse - plantenvermeerdering - forest trees - quercus robur - seeds - seed production - seed sources - seed trees - seed orchards - seed quality - pollination - fertilization - paternity - fathers - parentage - dna - genetic markers - genetic contamination - genetic analysis - propagation
    Om zaad van een zo hoog mogelijke genetische kwaliteit te verkrijgen worden zaadgaarden (aanplantingen van geselecteerde klonen voor de productie van zaad) zoveel mogelijk geïsoleerd van beplantingen van dezelfde soort, om achtergrondbestuiving te voorkomen. In de eikenzaadgaard 'Bremerberg' in Flevoland is d.m.v. vaderschapsanalyse met behulp van DNA-merkers (microsatellieten)onderzoek gedaan naar de mate van achtergrondbestuiving en de bijdrage van de verschillende klonen aan de bevruchting. Het merendeel van de eikels van de moederbomen blijkt bevrucht te zijn met stuifmeel van buiten de zaadgaard, maar dit blijkt geen afbreuk te doen aan de kwaliteit van het zaadgaardmateriaal. De consequenties voor aanleg en beheer van zaadgaarden worden besproken
    Vaderschapsanalyse bij eik : eikenstuifmeel komt van ver
    Bakker, E. ; Dam, B. van - \ 1999
    Nederlands Bosbouwtijdschrift 71 (1999)1. - ISSN 0028-2057 - p. 35 - 38.
    quercus - voortplanting - vaderschap - afstamming - stuifmeel - bestuiving - stuifmeelconcurrentie - bevruchting - selectieve bevruchting - genetische variatie - genetische analyse - quercus - reproduction - paternity - parentage - pollen - pollination - pollen competition - fertilization - selective fertilization - genetic variation - genetic analysis
    De eik houdt de genetische variatie op peil en voorkomt inteelt doordat de moedereik selecteert op stuifmeel van ver verwijderd staande eiken. Dit blijkt uit DNA-onderzoek van de eikels van groepjes eiken op locaties in het Leuvenumse bos en in Amsterdam
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