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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    Experimental demonstration of the benefits of somatic fusion and the consequences for allorecognition
    Bastiaans, E. ; Debets, A.J.M. ; Aanen, D.K. - \ 2015
    Evolution 69 (2015)4. - ISSN 0014-3820 - p. 1091 - 1099.
    vegetative incompatibility - neurospora-crassa - heterokaryon incompatibility - natural-populations - filamentous fungi - recognition - evolution - selection - genetics - cooperation
    Allorecognition, the ability to distinguish “self” from “nonself” based on allelic differences at allorecognition loci, is common in all domains of life. Allorecognition restricts the opportunities for social parasitism, and is therefore crucial for the evolution of cooperation. However, the maintenance of allorecognition diversity provides a paradox. If allorecognition is costly relative to cooperation, common alleles will be favored. Thus, the cost of allorecognition may reduce the genetic variation upon which allorecognition crucially relies, a prediction now known as “Crozier's paradox.” We establish the relative costs of allorecognition, and their consequences for the short-term evolution of recognition labels theoretically predicted by Crozier. We use fusion among colonies of the fungus Neurospora crassa, regulated by highly variable allorecognition genes, as an experimental model system. We demonstrate that fusion among colonies is mutually beneficial, relative to absence of fusion upon allorecognition. This benefit is due not only to absence of mutual antagonism, which occurs upon allorecognition, but also to an increase in colony size per se. We then experimentally demonstrate that the benefit of fusion selects against allorecognition diversity, as predicted by Crozier. We discuss what maintains allorecognition diversity
    Heritable Environmental Variance Causes Nonlinear Relationships Between Traits: Application to Birth Weight and Stillbirth of Pigs
    Mulder, H.A. ; Hill, W.G. ; Knol, E.F. - \ 2015
    Genetics 199 (2015)4. - ISSN 0016-6731 - p. 1255 - 1269.
    generalized linear-models - phenotypic variability - genetic-heterogeneity - residual variance - natural-populations - breeding values - litter size - body-size - selection - uniformity
    There is recent evidence from laboratory experiments and analysis of livestock populations that not only the phenotype itself, but also its environmental variance, is under genetic control. Little is known about the relationships between the environmental variance of one trait and mean levels of other traits, however. A genetic covariance between these is expected to lead to nonlinearity between them, for example between birth weight and survival of piglets, where animals of extreme weights have lower survival. The objectives were to derive this nonlinear relationship analytically using multiple regression and apply it to data on piglet birth weight and survival. This study provides a framework to study such nonlinear relationships caused by genetic covariance of environmental variance of one trait and the mean of the other. It is shown that positions of phenotypic and genetic optima may differ and that genetic relationships are likely to be more curvilinear than phenotypic relationships, dependent mainly on the environmental correlation between these traits. Genetic correlations may change if the population means change relative to the optimal phenotypes. Data of piglet birth weight and survival show that the presence of nonlinearity can be partly explained by the genetic covariance between environmental variance of birth weight and survival. The framework developed can be used to assess effects of artificial and natural selection on means and variances of traits and the statistical method presented can be used to estimate trade-offs between environmental variance of one trait and mean levels of others.
    Sex-biased inbreeding effects on reproductive success and home range size of the critically endangered black rhinoceros
    Cain, W.S. ; Wandera, A.B. ; Shawcross, S.G. ; Ouma, B.O. ; Watts, P.C. - \ 2014
    Conservation Biology 28 (2014)2. - ISSN 0888-8892 - p. 594 - 603.
    heterozygosity-fitness correlations - wide genetic diversity - natural-populations - diceros-bicornis - multilocus heterozygosity - microsatellite markers - wild populations - south-africa - depression - reserve
    A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically endangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring). Factors examined as predictors of reproductive success were age, home range size, number of nearby mates, reserve location, and multilocus heterozygosity (a proxy for inbreeding). Multilocus heterozygosity predicted male reproductive success (p<0.001, explained deviance >58%) and correlated with male home range size (p <0.01, r2 > 44%). Such effects were not apparent in females, where reproductive success was determined by age (p <0.01, explained deviance 34%) as females raise calves alone and choose between, rather than compete for, mates. This first report of a 3-way association between an individual male's heterozygosity, reproductive output, and territory size in a large vertebrate is consistent with an asymmetry in the level of intrasexual competition and highlights the relevance of sex-biased inbreeding for the management of many conservation-priority species. Our results contrast with the idea that wild populations of threatened taxa may possess some inherent difference from most nonthreatened populations that necessitates the use of detailed pedigrees to study inbreeding effects. Despite substantial variance in male reproductive success, the increased fitness of more heterozygous males limits the loss of heterozygosity. Understanding how individual differences in genetic diversity mediate the outcome of intrasexual competition will be essential for effective management, particularly in enclosed populations, where individuals have restricted choice about home range location and where the reproductive impact of translocated animals will depend upon the background distribution in individual heterozygosity. © 2013 Society for Conservation Biology.
    Epigenetic variation in asexually reproducing organisms
    Verhoeven, K.J.F. ; Preite, V. - \ 2014
    Evolution 68 (2014)3. - ISSN 0014-3820 - p. 644 - 655.
    dna methylation - arabidopsis-thaliana - japanese knotweed - transgenerational plasticity - phenotypic plasticity - transposable elements - natural-populations - fallopia-japonica - mutation-rates - clonal plants
    The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual–asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation.
    Development of a Nasonia vitripennis outbred laboratory population for genetic analysis
    Zande, L. van de; Ferber, S. ; Haan, A. de; Beukeboom, L.W. ; Heerwaarden, J. van; Pannebakker, B.A. - \ 2014
    Molecular Ecology Resources 14 (2014)3. - ISSN 1755-098X - p. 578 - 587.
    parasitoid wasp nasonia - local mate competition - sex-ratio - drosophila-melanogaster - natural-populations - ectoparasitic wasp - hymenoptera - genome - evolution - recombination
    The parasitoid wasp genus Nasonia has rapidly become a genetic model system for developmental and evolutionary biology. The release of its genome sequence led to the development of high-resolution genomic tools, for both interspecific and intraspecific research, which has resulted in great advances in understanding Nasonia biology. To further advance the utility of Nasonia vitripennis as a genetic model system and to be able to fully exploit the advantages of its fully sequenced and annotated genome, we developed a genetically variable and well-characterized experimental population. In this study, we describe the establishment of the genetically diverse HVRx laboratory population from strains collected from the field in the Netherlands. We established a maintenance method that retains genetic variation over generations of culturing in the laboratory. As a characterization of its genetic composition, we provide data on the standing genetic variation and estimate the effective population size (Ne ) by microsatellite analysis. A genome-wide description of polymorphism is provided through pooled resequencing, which yielded 417 331 high-quality SNPs spanning all five Nasonia chromosomes. The HVRx population and its characterization are freely available as a community resource for investigators seeking to elucidate the genetic basis of complex trait variation using the Nasonia model system
    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.
    Within-population genetic structure in beech (Fagus sylvatica L.) stands characterized by different disturbance histories: does forest management simplify population substructure?
    Piotti, A. ; Leonardi, S. ; Heuertz, M. ; Buiteveld, J. ; Geburek, T. ; Gerber, S. ; Kramer, K. ; Vettori, C. ; Vendramin, G.G. - \ 2013
    PLoS ONE 8 (2013)9. - ISSN 1932-6203 - 9 p.
    european beech - populus-trichocarpa - natural-populations - plant-populations - pollen dispersal - estimating seed - f-statistics - null alleles - douglas-fir - white-pine
    The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot hST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (FCluPlot = 0.067) was higher than the differentiation among the 10 plots (FPlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.
    A genetic linkage map for the South African angora goat
    Visser, C. ; Crooijmans, R.P.M.A. ; Marle Koster, E. Van - \ 2010
    Small Ruminant Research 93 (2010)2-3. - ISSN 0921-4488 - p. 171 - 179.
    natural-populations - sheep - genome - animals - breeds - locus
    Despite their economical importance, relatively few molecular studies have been made on goats compared to other livestock species. The most recent goat map was published in 1998, and lacks complete genome coverage. A large number of discrepancies and especially inter-chromosomal re-assignments were reported between the 1998 goat linkage map and the sheep map. In this study 94 microsatellite markers were amplified in 12 half-sib South African Angora goat families for compilation of a genetic map, aiming to confirm or reject previously reported rearrangements and to improve the alignment between the ovine and caprine maps. The number of informative meiosis per marker ranged from 69 to 836, with an average of 518. The microsatellites were mapped to 23 chromosomes, spanning 1352 cM and resulting in an average marker interval of 23.0 cM. Marker orders were compared to the previously published goat maps, as well as to the ovine map. Six chromosomes (CHI 2, 4, 5, 11, 13 and 19) showed rearrangements in marker order compared to the 1998 Schibler et al. goat map, while nine previously unmapped markers were conclusively assigned to eight chromosomes. Four of the previously reported intra-chromosomal rearrangements between the goat and sheep maps were confirmed to be either population specific or mapping errors. The verification of rearrangements in loci order will lead to improved alignment between the two maps, as well as improved efficiency of genome and fine mapping efforts in goats
    Genome-wide SNP detection in the great tit Parus major using high throughput sequencing
    Bers, N.E.M. van; Oers, K. van; Dibbits, B.W. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. - \ 2010
    Molecular Ecology 19 (2010)Suppl. s1. - ISSN 0962-1083 - p. 89 - 99.
    wild bird population - natural-populations - climate-change - linkage map - phenotypic plasticity - future-directions - genotyping assay - passerine bird - dna-sequences - evolution
    Identifying genes that underlie ecological traits will open exiting possibilities to study gene–environment interactions in shaping phenotypes and in measuring natural selection on genes. Evolutionary ecology has been pursuing these objectives for decades, but they come into reach now that next generation sequencing technologies have dramatically lowered the costs to obtain the genomic sequence information that is currently lacking for most ecologically important species. Here we describe how we generated over 2 billion basepairs of novel sequence information for an ecological model species, the great tit Parus major. We used over 16 million short sequence reads for the de novo assembly of a reference sequence consisting of 550 000 contigs, covering 2.5% of the genome of the great tit. This reference sequence was used as the scaffold for mapping of the sequence reads, which allowed for the detection of over 20 000 novel single nucleotide polymorphisms. Contigs harbouring 4272 of the single nucleotide polymorphisms could be mapped to a unique location on the recently sequenced zebra finch genome. Of all the great tit contigs, significantly more were mapped to the microchromosomes than to the intermediate and the macrochromosomes of the zebra finch, indicating a higher overall level of sequence conservation on the microchromosomes than on the other types of chromosomes. The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines.
    Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio
    Hooft, W.F. van; Prins, H.H.T. ; Getz, W.M. ; Jolles, A.E. ; Wieren, S.E. van; Greyling, B.J. ; Helden, P.D. ; Bastos, A.D.S. - \ 2010
    BMC Evolutionary Biology 10 (2010). - ISSN 1471-2148 - 11 p.
    cattle bos-taurus - syncerus-caffer - male-fertility - meiotic drive - bovine tuberculosis - drosophila-melanogaster - microsatellite analysis - natural-populations - sperm - selection
    Background - The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio. These sex-ratio (SR) genes modify (suppress) gamete transmission in their own favour at a fitness cost, allowing for stable polymorphism. Results - Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. Frequencies varied by a factor of five; too high to be alternatively explained by Y-chromosomal effects on pregnancy loss. Sex ratios were male-biased during wet and female-biased during dry periods (male proportion: 0.47-0.53), seasonally and annually. Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. Conclusions - The distinctive properties suggested for explaining Y-chromosomal polymorphism in African buffalo may not be restricted to this species alone. SR genes may play a broader and largely overlooked role in mammalian sex-ratio variation
    The reintroduction of the Eurasian otter (Lutra lutra) into the Netherlands: hidden life revealed by noninvasive genetic monitoring
    Koelewijn, H.P. ; Pérez-Haro, M. ; Jansman, H.A.H. ; Boerwinkel, M.C. ; Bovenschen, J. ; Lammertsma, D.R. ; Niewold, F.J.J. ; Kuiters, A.T. - \ 2010
    Conservation Genetics 11 (2010)2. - ISSN 1566-0621 - p. 601 - 614.
    natural-populations - individual identification - conservation genetics - spatial-organization - microsatellite loci - genotyping feces - eastern germany - dna - size - biology
    The last recorded presence of the Eurasian otter (Lutra lutra) in the Netherlands dates from 1989 and concerned a dead individual. In 2002 a reintroduction programme was started, and between June 2002 and April 2008 a total of 30 individuals (10 males and 20 females) were released into a lowland peat marsh in the north of the Netherlands. Noninvasive genetic monitoring based on the genetic profiles obtained from DNA extracted from otter faeces (spraints) was chosen for the post-release monitoring of the population. To this end, the founding individuals were genotyped before release and spraints were collected in the release area each winter from 2002 to 2008. From June 2002 to April 2008 we analysed the genetic profile of 1,265 spraints on the basis of 7–15 microsatellite loci, 582 of which (46%) were successfully assigned to either released or newly identified genotypes. We identified 54 offspring (23 females and 31 males): the females started to reproduce after 2 years and the males after 4 years. The mating and reproductive success among males was strongly skewed, with a few dominant males fathering two-thirds of the offspring, but the females had a more even distribution. The effective population size (Ne) was only about 30% of the observed density (N), mainly because of the large variance in reproductive success among males. Most juvenile males dispersed to surrounding areas on maturity, whereas juvenile females stayed inside the area next to the mother’s territory. The main cause of mortality was traffic accidents. Males had a higher mortality rate (22 out of 41 males (54%) vs. 9 out of 43 females (21%)). During winter 2007/08 we identified 47 individuals, 41 of which originated from mating within the release area. This study demonstrates that noninvasive molecular methods can be used efficiently in post-release monitoring studies of elusive species to reveal a comprehensive picture of the state of the population
    Phylogenetic and biological species diversity within the Neurospora tetrasperma complex
    Menkis, A. ; Bastiaans, E. ; Jacobson, D.J. ; Johannesson, H. - \ 2009
    Journal of Evolutionary Biology 22 (2009)9. - ISSN 1010-061X - p. 1923 - 1936.
    mating-type chromosome - het-c locus - natural-populations - sexual dysfunction - model eukaryote - fungi - recognition - evolution - strains - heterothallism
    The objective of this study was to explore the evolutionary history of the morphologically recognized filamentous ascomycete Neurospora tetrasperma, and to reveal the genetic and reproductive relationships among its individuals and populations. We applied both phylogenetic and biological species recognition to a collection of strains representing the geographic and genetic diversity of N. tetrasperma. First, we were able to confirm a monophyletic origin of N. tetrasperma. Furthermore, we found nine phylogenetic species within the morphospecies. When using the traditional broad biological species recognition all investigated strains of N. tetrasperma constituted a single biological species. In contrast, when using a quantitative measurement of the reproductive success, incorporating characters such as viability and fertility of offspring, we found a high congruence between the phylogenetic and biological species recognition. Taken together, phylogenetically and biologically defined groups of individuals exist in N. tetrasperma, and these should be taken into account in future studies of its life history traits.
    The effect of sheltered load on reproduction in Solanum carolinense, a species with variable self-incompatibility
    Mena-Ali, J.I. ; Keser, L.H. ; Stephenson, A.G. - \ 2009
    Sexual Plant Reproduction 22 (2009)2. - ISSN 0934-0882 - p. 63 - 71.
    pollen-tube growth - inbreeding depression - flowering plants - natural-populations - nicotiana-alata - s-alleles - evolution - solanaceae - model - fertilization
    In previous studies, we have investigated the strength of self-incompatibility (SI) in Solanum carolinense, a highly successful weed with a fully functional SI system that inhabits early successional and other disturbed habitats. We have found that the SI response in S. carolinense is a plastic trait—its strength being affected by the age of the flowers, and the presence of developing fruits and that there are genetic differences among families in their self-fertility. However, in species with a fully functional SI response, selfing would not be that common. As a result, deleterious recessives scattered though the genome of horsenettle are only occasionally exposed to selection. It has been suggested that deleterious recessives accumulate near S-alleles in strong SI species because the S-locus is located in a non-recombining region of the genome and because strong S-alleles are never in the homozygous state, thus sheltering some of the genetic load near the S-locus from selection. We performed a series of laboratory and greenhouse experiments to determine the extent to which sheltered load adds to the overall magnitude of inbreeding depression in horsenettle. Specifically, we amplified and sequenced the S-alleles from 16 genets collected from a large population in Pennsylvania and performed a series of controlled self-pollinations. We then grew the selfed progeny in the greenhouse; recorded various measures of growth and reproductive output; and amplified and sequenced their S-allele(s). We found that the heterozygous progeny of self-pollinations produce more flowers and have a greater ability to set both self and cross seed than S-homozygous progeny. We also found evidence of variation in the magnitude of load among S-alleles. These results suggest that sheltered load might slow the fixation of weak (partially compatible) S-alleles in this population, thus adding to the maintenance of a mixed mating system rather than leading to the fixation of the selfing alleles
    Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population.
    Bink, M.C.A.M. ; Anderson, A.D. ; Weg, W.E. van de; Thompson, E.A. - \ 2008
    Theoretical and Applied Genetics 117 (2008)6. - ISSN 0040-5752 - p. 843 - 855.
    maximum-likelihood - molecular markers - natural-populations - heritability - coefficients - individuals - information
    Several estimators have been proposed that use molecular marker data to infer the degree of relatedness for pairs of individuals. The objective of this study was to evaluate the performance of seven estimators when applied to marker data of a set of 33 key individuals from a large complex apple pedigree. The evaluation considered different scenarios of allele frequencies and different numbers of marker loci. The method of moments estimators were Similarity, Queller-Goodknight, Lynch-Ritland and Wang. The maximum likelihood estimators were Thompson, Anderson-Weir and Jacquard. The pedigree-based coancestry coefficients were taken as the point of reference in calculating correlations and root mean square error (RMSE). The marker data comprised 86 multi-allelic SSR markers on 17 linkage groups, covering 11 Morgans. Additionally, we simulated 10 datasets conditional on the real pedigree to support the results on the real dataset. None of the estimators outperformed the others. Knowledge of allele frequencies appeared to be the most influential, i.e., the highest correlations and lowest RMSE were found when frequencies from the founder population were available. When equal allele frequencies were used, all estimators resulted in very similar, but on average lower, correlations. The use of allele frequencies estimated from the set of 33 individuals gave, on average, the poorest results. The maximum likelihood estimators and the Lynch-Ritland estimator were the most sensitive to allele frequencies. The results from the simulation study fully supported the trends in results of the real dataset. This study indicated that high correlations (up to 0.90) and small RMSE (below 0.03), may be obtained when population allelic frequencies are available. In this scenario, the performances of the various estimators were similar, but seemed to favor the maximum likelihood estimators. In the absence of reliable allele frequencies the method of moments estimators were shown to be more robust. The number of marker loci influenced the average performance of the estimators; however, the ranking was not affected. Correlations up to 0.80 were obtained when two markers per chromosome and appropriate allele frequencies were available. Adding more markers to the current dataset may lead to marginal improvements.
    The Contribution of Social Effects to Heritable Variation in Finishing Traits of Domestic Pigs (Sus scrofa)
    Bergsma, R. ; Kanis, E. ; Knol, E.F. - \ 2008
    Genetics 178 (2008)3. - ISSN 0016-6731 - p. 1559 - 1570.
    multiple-hen cages - group selection - kin selection - genetic-parameters - multilevel selection - natural-populations - variance-components - molecular markers - biological groups - model
    Social interactions among individuals are ubiquitous both in animals and in plants, and in natural as well as domestic populations. These interactions affect both the direction and the magnitude of responses to selection and are a key factor in evolutionary success of species and in the design of breeding schemes in agriculture. At present, however, very little is known of the contribution of social effects to heritable variance in trait values. Here we present estimates of the direct and social genetic variance in growth rate, feed intake, back fat thickness, and muscle depth in a population of 14,032 domestic pigs with known pedigree. Results show that social effects contribute the vast majority of heritable variance in growth rate and feed intake in this population. Total heritable variance expressed relative to phenotypic variance was 71% for growth rate and 70% for feed intake. These values clearly exceed the usual range of heritability for those traits. Back fat thickness and muscle depth showed no heritable variance due to social effects. Our results suggest that genetic improvement in agriculture can be substantially advanced by redirecting breeding schemes, so as to capture heritable variance due to social effects.
    Bridging the gap between ecophysiological and genetic knowledge to assess the adaptive potential of European beech
    Kramer, K. ; Buiteveld, J. ; Forstreuter, M. ; Geburek, T. ; Leonardi, S. ; Menozzi, P. ; Povillon, F. ; Schelhaas, M.J. ; Teissier du Cros, E. ; Vendramin, G.G. ; Werf, D.C. van der - \ 2008
    Ecological Modelling 216 (2008)3-4. - ISSN 0304-3800 - p. 333 - 353.
    fagus-sylvatica l. - mating system parameters - natural-populations - shade tolerance - climate-change - postglacial recolonization - species distribution - british beechwoods - field-measurements - ecological theory
    In this study we aimed to combine knowledge of the ecophysiology and genetics of European beech to assess the potential of this species to adapt to environmental change. Therefore, we performed field and experimental studies on the genetic and ecophysiological functioning of beech. This information was integrated through a coupled genetic¿ecophysiological model for individual trees that was parameterized with information derived from our own studies or from the literature. Using the model, we evaluated the adaptive response of beech stands in two ways: firstly, through sensitivity analyses (of initial genetic diversity, pollen dispersal distance, heritability of selected phenotypic traits, and forest management, representing disturbances) and secondly, through the evaluation of the responses of phenotypic traits and their genetic diversity to four management regimes applied to 10 study plots distributed over Western Europe. The model results indicate that the interval between recruitment events strongly affects the rate of adaptive response, because selection is most severe during the early stages of forest development. Forest management regimes largely determine recruitment intervals and thereby the potential for adaptive responses. Forest management regimes also determine the number of mother trees that contribute to the next generation and thereby the genetic variation that is maintained. Consequently, undisturbed forests maintain the largest amount of genetic variation, as recruitment intervals approach the longevity of trees and many mother trees contribute to the next generation. However, undisturbed forests have the slowest adaptive response, for the same reasons. Gene flow through pollen dispersal may compensate for the loss in genetic diversity brought about by selection. The sensitivity analysis showed that the total genetic diversity of a 2 ha stand is not affected by gene flow if the pollen distance distribution is varied from highly left-skewed to almost flat. However, a stand with a prevailing short-distance gene flow has a more pronounced spatial genetic structure than stands with equal short- and long-distance gene flows. The build-up of a spatial genetic structure is also strongly determined by the recruitment interval. Overall, the modelling results indicate that European beech has high adaptive potential to environmental change if recruitment intervals are short and many mother trees contribute to the next generation. The findings have two implications for modelling studies on the impacts of climate change on forests. Firstly: it cannot be taken for granted that parameter values remain constant over a time horizon of even a few generations ¿ this is particularly important for threshold values subject to strong selection, like budburst, frost hardiness, drought tolerance, as used in species area models. Secondly: forest management should be taken into account in future assessments, as management affects the rate of adaptive response and thereby the response on trees and forests to environmental change, and because few forests are unmanaged. We conclude that a coupled ecophysiological and quantitative genetic tree model is a useful tool for such studies
    Genetic diversity of maize (Zea mays L. ssp. mays) in communities of the western highlands of Guatemala: geographical patterns and processes.
    Etten, J. van; Fuentes, M.R. ; Molina, L.G. ; Ponciano, K.M. - \ 2008
    Genetic Resources and Crop Evolution 55 (2008)2. - ISSN 0925-9864 - p. 303 - 317.
    natural-populations - similarity - markers - mexico - flow
    This study concerns spatial genetic patterning, seed flow and the impact of modern varieties in maize populations in Chimaltenango, Guatemala. It uses a collection of 79 maize seed samples from farmers in the area and five samples derived from modern varieties. Bulked SSR markers employed with bulked samples (ten plants) were used. Genetic distances between populations based on these SSR data were used as a measure of co-ancestry. The study describes the genetic variation in space, assesses the association of maize diversity with spatial and environmental descriptors and quantitative traits, and provides a test of the impact of improved varieties. Maize diversity showed significant isolation-by-distance locally, but not regionally. This was interpreted as evidence for a difference between local and regional mechanisms of seed exchange; regional exchange is more related to innovation. There was also a significant association with altitude and ear/grain characteristics (related to racial classifications). Also, consistent evidence for the influence of modern varieties of maize was found, although its impact was limited spatially. It is argued that the spatial distributions of maize diversity are important to consider for germplasm collection, but should be seen as a recent outcome of dynamic processes.
    Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster
    Kuang, H. ; Eck, H.J. van; Sicard, D. ; Michelmore, R. ; Nevo, E. - \ 2008
    Genetics 178 (2008)3. - ISSN 0016-6731 - p. 1547 - 1558.
    mildew bremia-lactucae - arabidopsis-thaliana - natural-populations - wild lactuca - cultivated lettuce - molecular evolution - statistical tests - encoding genes - major cluster - diversity
    Genetic structure and diversity of natural populations of prickly lettuce (Lactuca serriola) were studied using AFLP markers and then compared with the diversity of the RGC2 disease resistance gene cluster. Screening of 696 accessions from 41 populations using 319 AFLP markers showed that eastern Turkish and Armenian populations were the most diverse populations and might be located in the origin and center of diversity of L. serriola. Screening 709 accessions using the microsatellite MSATE6 that is located in the coding region of most RGC2 homologs detected 366 different haplotypes. Again, the eastern Turkish and Armenian populations had the highest diversities at the RGC2 cluster. The diversities at the RGC2 cluster in different populations were significantly correlated with their genomewide diversities. There was significant variation of copy number of RGC2 homologs in different populations, ranging from 12 to 22 copies per genome. The nucleotide diversities of two conserved lineages (type II) of RGC2 genes (K and L) were not correlated with diversities calculated using the MSATE6 or AFLP data. We hypothesize that the high genomewide diversity and diversity of the RGC2 cluster in eastern Turkish and Armenian populations resulted from high abiotic and biotic stresses in the regions of origin of L. serriola.
    Structure of the genetic diversity in Black poplar (Populus nigra L.) populations across European river systems: consequences for conservation and restoration
    Smulders, M.J.M. ; Cottrell, J.E. ; Lefevre, F. ; Schoot, J. van der; Arens, P.F.P. ; Vosman, B. ; Tabbener, H.E. ; Grassi, F. ; Fossati, T. ; Castiglione, S. ; Krystufek, V. ; Fluch, S. ; Burg, K. ; Vornam, B. ; Pohl, A. ; Gebhardt, K. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Volosyanchuck, R. ; Pospiskova, M. ; Bordacs, S. ; Bovenschen, J. ; Dam, B.C. van; Koelewijn, H.P. ; Halfmaerten, D. ; Ivens, B. ; Slycken, J. Van; Vanden Broeck, A. ; Storme, V. ; Boerjan, W. - \ 2008
    Forest Ecology and Management 255 (2008)5-6. - ISSN 0378-1127 - p. 1388 - 1399.
    fragment length polymorphism - microsatellite markers - natural-populations - aflp markers - linkage maps - dispersal - stands - reproduction - tremuloides - salicaceae
    Black poplar (Populus nigra L.) is a keystone species for riparian ecosystems in Europe. We analysed the structure of genetic diversity of 17 populations from 11 river valleys that are part of seven catchment systems (Danube, Ebro, Elbe, Po, Rhine, Rhone, and Usk) in Europe, in relation to geography and river management. In total, 1069 trees were genotyped using AFLP and microsatellite markers. The trees had an observed heterozygosity of 0.74 (range 0.59¿0.82 across microsatellite loci). The majority (72.6¿90.8%, depending on the marker system) of the genetic variation was present within populations. Most pairs of populations along a river were relatively similar (pairwise Fst 0.042¿0.135 based on AFLP, 0.002¿0.037 based on microsatellites). Overall population differentiation among rivers was considerable (Fst among populations was 0.268 based on AFLP, and 0.081 based on microsatellites). An analysis using the program Structure indicated that all populations recruited plants from several clusters. Geographically close populations tended to draw from the same Structure clusters, including populations from adjacent catchments. The Danube and Inn populations in Austria were genetically more similar to the Vltava population (Elbe catchment) in Czech Republic than the geographically more distant populations along the Tisa and Prut rivers of the Danube catchment in Ukraine. This indicates that gene flow and dispersal takes place across fairly large distances and between river catchments. Consistent with this result, a principal coordinate analysis of genetic distances among individual trees based on AFLP bands showed large overlap of populations, although the French and Spanish samples formed distinct clusters, and the samples from the Ticino (Italy) were at an intermediate position. The extent of clonal duplication was highest along regulated rivers, with e.g., 41% clonal duplication along the Rhine in The Netherlands (up to 32 trees for one genet). The Usk contained a man-made population (two genotypes along the entire river, one genet present as 70 trees out of 72 trees sampled). No clonal duplication was found along dynamic rivers, such as the Ebro (Spain), the Drome (France), and the Tisa and Prut (Ukraine).
    Acquisition and ecological characterization of Lactuca serriola L. germplasm collected in the Czech Republic, , Germany, the Netherlands and United Kingdom
    Lebeda, A. ; Dolezalova, I. ; Kristkova, E. ; Dehmer, K.J. ; Astley, D. ; Wiel, C.C.M. van de; Treuren, R. van - \ 2007
    Genetic Resources and Crop Evolution 54 (2007)3. - ISSN 0925-9864 - p. 555 - 562.
    natural-populations - bremia-lactucae - asteraceae - spp.
    Expeditions were conducted in the Czech Republic, Germany, the Netherlands and United Kingdom in 2001 (partly 1998) to study Lactuca serriola L. (prickly lettuce, compass plant) geographic distribution, ecology, habitat characteristics and occurrence of diseases and pests on this species. During these missions the seed material of L. serriola L. was collected in an east¿west transect of these four countries. The European transect where seeds were collected and field observations were made represents a relatively large area between 2°34¿50¿¿ W¿17°32¿46¿¿ E and 47°40¿42¿¿¿54°04¿19¿¿ N. The seed material was used for regeneration, inclusion in the national genetic resources collections of individual countries and for research purposes in follow-up studies. During the missions, 50 locations with occurrence of L. serriola L. were visited (16 in Czech Republic and Germany, 10 in UK and 8 in the Netherlands). Individual seed lots of sixteen different plants were collected at each location (L. serriola L. population). Thus, in total 800 seed samples were collected. In Czech Republic and Germany L. serriola L. f. serriola dominated in all observed populations, in the Netherlands both f. serriola and f. integrifolia occurred in pure or mixed stands, whereas in the United Kingdom L. serriola L. f. integrifolia (S.F. Gray) S.D. Prince et R.N. Carter was dominant. L. serriola L. was recorded at various altitudes (¿4 to 410 m), different habitats (ditches, along roads, fields and field margins, ruderal places, pavements and parking sites, fallow fields), individual populations varied substantially in size (20 to >1000 plants), area covered (25¿10,000 m2), and the structure and character of associated plant communities. Natural infections by downy mildew (Bremia lactucae Regel) and powdery mildew (Golovinomyces cichoracearum (DC.) V.P. Gelyuta) were observed in some populations. B. lactucae Regel was recorded only in Czech Republic, G. cichoracearum (DC.) V.P. Gelyuta was more common in continental Europe. General and specific aspects of L. serriola L. geographic distribution and ecology are discussed.
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