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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    Genetic and morphological diversity of okra (Abelmoschus esculentus [L.] Moench.) genotypes and their possible relationships, with particular reference to Greek landraces
    Kyriakopoulou, O.G. ; Arens, P.F.P. ; Pelgrom, K.T.B. ; Karapanos, I. ; Bebeli, P. ; Passam, H.C. - \ 2014
    Scientia Horticulturae 171 (2014). - ISSN 0304-4238 - p. 58 - 70.
    numerical-analysis - germplasm - aflp - collection - cultivars - stability - patterns - distance - markers - plants
    Despite its high economic value in many countries (especially in developing regions of the tropics and sub-tropics), okra has received little attention with respect to its source of origin and genetic diversity, particularly at the molecular level. Phenotypic description (morphology, pod characteristics and seed germination) and AFLP (amplified fragment length polymorphism) analysis were performed on Greek and international genotypes. Whereas morphological descriptors did not separate the accessions according to their geographical origin, AFLP analysis revealed a low level (12%) of polymorphism and distinct geographical groupings. Greek germplasm separated into three distinct groups with no overlap between them on the basis of molecular markers. A higher degree of genetic heterogeneity was found (UPGMA analysis) among the accessions of the Boyiatiou group than in the Pylaias group, whereas the occurrence of some common phylogenetic characteristics made separation on the basis of morphology alone difficult. The results from AFLP markers indicate that Greek germplasm constitutes a significant pool of variation with respect to morphological parameters, pod characteristics and seed germinability. Moreover, differences in seed germination among phenotypes may relate to their geographical origin (mainland or islands).
    Range of attraction of a 6-W moth light trap
    Grunsven, R.H.A. van; Lham, D. ; Geffen, K.G. van; Veenendaal, E.M. - \ 2014
    Entomologia Experimentalis et Applicata 152 (2014)1. - ISSN 0013-8703 - p. 87 - 90.
    lepidoptera - conservation - distance - catches - decline
    Validation of isovist variables as predictors of perceived landscape openness
    Weitkamp, S.G. ; Lammeren, R.J.A. van; Bregt, A.K. - \ 2014
    Landscape and Urban Planning 125 (2014). - ISSN 0169-2046 - p. 140 - 145.
    preference - space - permeability - indicators - enclosure - distance - impacts
    This paper tests the quality of calculated 2D isovist variables as predictors of perceived landscape openness. An isovist is the calculated field of view from a given viewpoint in space. Three isovist variables were selected to estimate openness: the minimum radial, the maximum radial and the average radial. An experiment with 32 participants was conducted to compare values of these calculated variables with perceived openness. The comparison showed that two variables, the maximum radial and average radial, explained most of the variation of perceived openness for groups and individuals. The three calculated isovist variables were strongly correlated to their measured equivalents in the field, which were obtained with a binocular with a rangefinder. The isovist variables also showed strong correlations with their perceived equivalents obtained by the perception of the 32 participants, except at very long distances. This research shows that the selected isovist variables are good indicators for perceived landscape openness.
    Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data
    Heerwaarden, J. van; Odong, T.L. ; Eeuwijk, F.A. van - \ 2013
    Theoretical and Applied Genetics 126 (2013)3. - ISSN 0040-5752 - p. 763 - 772.
    population-structure - germplasm collections - model - distance - conservation - accessions - algorithms - management - diversity - richness
    Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups.
    Do distant foods decrease intake? The effect of food accessibility on consumption
    Maas, Josje ; Ridder, Denise T.D. de; Vet, Emely de; Wit, John B.F. de - \ 2012
    Psychology and Health 27 (2012)SUPPL. 2. - ISSN 0887-0446 - p. 59 - 73.
    distance - food accessibility - food intake - obesogenic environment

    Objective: Two studies examined the hypothesis that making snacks less accessible contributes to the regulation of food intake. Study 1 examined whether decreasing the accessibility of snacks reduces probability and amount of snack intake. The aim of Study 2 was to replicate the results and explore the underlying mechanism in terms of perceived effort to obtain the snack and perceived salience of the snack.Methods: In Study 1 (N = 77) and Study 2 (N = 54) distance to a bowl of snacks was randomly varied at 20, 70 or 140 cm in an experimental between-subjects design. Main outcome measures were the number of people who ate any snacks (probability of snack intake), the amount of snacks consumed and risk of compensatory behaviour as measured by food craving. In Study 2, self-report ratings of salience and effort were examined to explore potential underlying mechanisms.Results: Study 1 showed lower probability and amount of intake in either of more distant conditions (70 and 140 cm) compared to the proximal condition (20 cm), with no unintended effects in terms of increased craving. Study 2 replicated the results of Study 1 and showed that distance affected perceived effort but not salience.Conclusions: Making snacks less accessible by putting them further away is a potentially effective strategy to decrease snack intake, without risk of compensatory behaviour.

    Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra)
    Jiao, Y. ; Jia, H.M. ; Li, X.W. ; Chai, M.L. ; Jia, H.J. ; Chen, Z. ; Wang, G.Y. ; Chai, C.Y. ; Weg, W.E. van de; Gao, Z.S. - \ 2012
    BMC Genomics 13 (2012). - ISSN 1471-2164
    genetic diversity - microsatellite markers - whole-genome - distance - dna - l.
    Background: Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in recent years has stimulated its extension in China and introduction to Australia. A limited number of co-dominant markers have been developed and applied in genetic diversity and identity studies. Here we report, for the first time, a survey of whole genome shotgun data to develop a large number of simple sequence repeat (SSR) markers to analyse the genetic diversity of the common cultivated Chinese bayberry and the relationship with three other Myrica species. Results: The whole genome shotgun survey of Chinese bayberry produced 9.01Gb of sequence data, about 26x coverage of the estimated genome size of 323 Mb. The genome sequences were highly heterozygous, but with little duplication. From the initial assembled scaffold covering 255 Mb sequence data, 28,602 SSRs (>= 5 repeats) were identified. Dinucleotide was the most common repeat motif with a frequency of 84.73%, followed by 13.78% trinucleotide, 1.34% tetranucleotide, 0.12% pentanucleotide and 0.04% hexanucleotide. From 600 primer pairs, 186 polymorphic SSRs were developed. Of these, 158 were used to screen 29 Chinese bayberry accessions and three other Myrica species: 91.14%, 89.87% and 46.84% SSRs could be used in Myrica adenophora, Myrica nana and Myrica cerifera, respectively. The UPGMA dendrogram tree showed that cultivated Myrica rubra is closely related to Myrica adenophora and Myrica nana, originating in southwest China, and very distantly related to Myrica cerifera, originating in America. These markers can be used in the construction of a linkage map and for genetic diversity studies in Myrica species. Conclusion: Myrica rubra has a small genome of about 323 Mb with a high level of heterozygosity. A large number of SSRs were identified, and 158 polymorphic SSR markers developed, 91% of which can be transferred to other Myrica species.
    Geospatial analysis of species, biodiversity and landscapes: Introduction to the second special issue on spatial ecology
    Laffan, S.W. ; Skidmore, A.K. ; Franklin, J. - \ 2012
    International Journal of Geographical Information Science 26 (2012)11. - ISSN 1365-8816 - p. 2003 - 2007.
    habitat - models - scale - distributions - conservation - uncertainty - diversity - distance - overlap - disease
    Communication in the Third Dimension: Song Perch Height of Rivals Affects Singing Response in Nightingales
    Sprau, P. ; Roth, T. ; Naguib, M. ; Amrhein, V. - \ 2012
    PLoS ONE 7 (2012)3. - ISSN 1932-6203
    broad-band trills - pairing success - phylloscopus-trochilus - luscinia-megarhynchos - pied flycatcher - territory - distance - location - choice - signal
    Many animals use long-range signals to compete over mates and resources. Optimal transmission can be achieved by choosing efficient signals, or by choosing adequate signalling perches and song posts. High signalling perches benefit sound transmission and reception, but may be more risky due to exposure to airborne predators. Perch height could thus reflect male quality, with individuals signalling at higher perches appearing as more threatening to rivals. Using playbacks on nightingales (Luscinia megarhynchos), we simulated rivals singing at the same height as residents, or singing three metres higher. Surprisingly, residents increased song output stronger, and, varying with future pairing success, overlapped more songs of the playback when rivals were singing at the same height than when they were singing higher. Other than expected, rivals singing at the same height may thus be experienced as more threatening than rivals singing at higher perches. Our study provides new evidence that territorial animals integrate information on signalling height and thus on vertical cues in their assessment of rivals.
    Is spatial structure the key to promote plant diversity in Mediterranean forets plantations?
    González-Moreno, P. ; Quero, J.L. ; Poorter, L. ; Bonet, F.J. ; Zamora, R. - \ 2011
    Basic and Applied Ecology 12 (2011)3. - ISSN 1439-1791 - p. 251 - 259.
    pine plantations - seed dispersal - fragments - restoration - recruitment - vegetation - patterns - distance - spain - edge
    Mediterranean forest plantations are currently under an intense debate related to their ecological function, sustainability and future performance. In several Mediterranean countries, efforts are directed to convert pine plantations into mixed and more diverse forests. This research aims to evaluate the effect of the spatial configuration of pine plantations on regeneration and plant diversity in order to facilitate plantation management towards more diversified stands. Spatial characteristics of plantations (proximity to different vegetation types, fragmentation and internal patch structure) were related to abundance of seedlings of an ecologically important broadleaved species, Holm Oak (Quercus ilex L.), and the Shannon diversity index of the community. Q. ilex seedling abundance and plant diversity in pine plantation patches are favoured by the proximity to oak patches located uphill. Fragmentation affected only plant diversity, with smaller patches having more diversity. The internal structure of the pine patch influenced both regeneration of Q. ilex and diversity. Pine patches with lower pine tree density were characterized by higher diversity and less Q. ilex regeneration confirming that internal structure affects species differently. From a management perspective, the process of conversion of Mediterranean pine plantations to mixed oak–pine forests could be facilitated by (1) having the seed source uphill from the plantation, (2) increasing the fragmentation of plantations and (3) promoting the internal heterogeneity of plantations to create a diverse range of light environments matching the different requirements of species
    Spatial variation in ditch bank plant species composition at the regional level: the role of environment and dispersal
    Leng, X. ; Musters, C.J.M. ; Snoo, G.R. de - \ 2010
    Journal of Vegetation Science 21 (2010)5. - ISSN 1100-9233 - p. 868 - 875.
    seed dispersal - beta-diversity - similarity - distance - conservation - patterns - ecology - communities - biodiversity - forests
    Questions: Can patterns of species similarity on ditch banks be explained by environmental and dispersal factors and, if so, to what extent? Does the pattern of distance decay differ among different species groups (all species versus target species of conservation interest; species of different dispersal type)? Location: Krimpenerwaard, the Netherlands. Methods: In 2006-2007, ditch bank vegetation data on 130 terrestrial herbaceous species were collected on 72 plots. Species similarity was measured and related to environmental distance (soil type and nutrient level) and dispersal distance (geographic distance and limitation of dispersal by water, wind and agricultural activities) as explanatory factors using multiple regression on distance matrices (MRM). Differences in rates of distance decay in species similarity among different subsets of data (species groups) were investigated using randomization tests. Results: In all species, patterns of similarity of composition are influenced mainly by variations in dispersal, while for target species these are due to combined effects of environmental and dispersal variation. Compared with species using other dispersal mechanisms, water-dispersed species had half the rate of distance decay. Conclusions: For all species considered here, dispersal limitation seems more responsible for the spatial variation in species composition than environmental determinism. Conservation management focused on plant species diversity would be more successful in areas adjacent to those where a similar management regime is already in force. For target species of conservation interest, besides dispersal limitation, environmental determinants like nutrient level are also important. As a means of conserving such target species, therefore, focusing on reducing nutrient levels and facilitating species dispersal will be more effective than current management practices, which mainly focus on reducing fertilizer inputs.
    Postdispersal seed predation and seed viability in forest soils: implications for the regeneration of tree species in Ethiopian church forests
    Wassie Eshete, A. ; Bekele, T. ; Sterck, F.J. ; Teketay, D. ; Bongers, F. - \ 2010
    African Journal of Ecology 48 (2010)2. - ISSN 0141-6707 - p. 461 - 471.
    europaea ssp-cuspidata - tropical rain-forest - germination ecology - northern ethiopia - prunus-africana - fragments - distance - rodents - edge - microhabitat
    Almost all dry Afromontane forests of Northern Ethiopia have been converted to agricultural, grazing or scrub lands except for small fragments left around churches ('Church forests'). Species regeneration in these forests is limited. We investigated (i) how intense postdispersal seed predation was in church forest, and if this seed predation varied with species and/or habitat, and (ii) for how long tree seeds maintained their viability while buried in forest soil. In the seed predation experiment, we monitored seeds of six tree species in four habitats for a period of 14 weeks (the peak seeding season). In the seed viability experiment, we assessed seed viability of five species in four habitats after being buried 6, 12, or 18 months. Ninety-two percent of the tree seeds were predated within 3.5 months. Predation was mainly dependent on species whereas habitat had a weaker effect. Seed viability decreased sharply with burial time in soil for all species except for Juniperus. To minimize seed availability limitation for regeneration of such species in the forest, the standing vegetation needs to be persistently managed and conserved for a continuous seed rain supply. Additional seed sowing, and seed and seedling protection (by e.g. animal exclosures) may increase successful regeneration of important species in these forests
    Effects of landscape structure on genetic diversity of Geum urbanum L. populations in agricultural landscapes
    Schmidt, T. ; Arens, P.F.P. ; Smulders, M.J.M. ; Billeter, R. ; Liira, J. ; Augenstein, I. ; Durka, W. - \ 2009
    Flora 204 (2009)7. - ISSN 0367-2530 - p. 549 - 559.
    habitat fragmentation - f-statistics - land-use - flow - distance - biodiversity - asteraceae - ecology - systems - europe
    Plant species in fragmented populations are affected by landscape structure because persistence within and migration among inhabited patches may be influenced by the identity and configuration of surrounding habitat elements. This may also be true for species of the semi-natural vegetation in agricultural landscapes. To determine the effect of landscape elements we analyzed Wood Avens (Geum urbanum L.) populations within three 4×4 km2 agricultural landscapes in Germany, Switzerland and Estonia, which differ in levels of land use intensity and habitat fragmentation. Genetic variation was determined in 15 randomly selected populations in each landscape using 10 microsatellite loci. The landscape structure was assessed at two circles around each population, with radii defined by the range limits of spatial genetic autocorrelation. Multiple regression analysis was used to determine the influence of landscape structure variables for inter- and intrapopulation genetic diversity. Gene diversity was equally high in Germany (He=0.27) and Switzerland (He=0.26) but lower in Estonia (He=0.16). A high overall inbreeding coefficient (FIS=0.89) was found, as expected for a selfing breeding system in G. urbanum. Genetic differentiation among populations was high (overall FST=0.43, 0.48, and 0.45 in Estonia, Switzerland and Germany, respectively), and did not differ among the three landscapes. Only a moderate influence of individual land use types on genetic diversity within and among populations was found with some idiosyncratic relationships. Genetic variation within populations was correlated to the amount of hedgerows positively in Estonia but negatively in Switzerland. The study demonstrates that the distribution of individual land use types affects the genetic pattern of a common plant species. However, different variables were identified to influence the genetic structure in three different landscapes. This indicates a major influence of landscape-specific land use history and stochastic processes determining gene flow and plant population structure
    Economic valuation of habitat defragmentation: A study of the Veluwe, the Netherlands
    Heide, C.M. van der; Bergh, J.C.J.M. van den; Ierland, E.C. van; Nunes, P.A.L.D. - \ 2008
    Ecological Economics 67 (2008)2. - ISSN 0921-8009 - p. 205 - 216.
    natuurbescherming - kosten - natuurreservaten - natuurontwikkeling - ecologische hoofdstructuur - habitatfragmentatie - natuur - veluwe - nature conservation - costs - nature reserves - nature development - ecological network - habitat fragmentation - nature - veluwe - options allowing respondents - contingent valuation - express uncertainty - multiple bids - values - distance - wtp
    This paper offers an economic value assessment of a nature protection programme in the Veluwe, the Netherlands. This programme involves two defragmentation scenarios: the first scenario connects the central part of the Veluwe with river forelands in a north-eastern direction (i.e. the meadows of the IJssel river), while the second scenario is focussed on defragmentation in a south-western direction (i.e. the meadows of the Rhine river). The valuation is based on a questionnaire that was administered during face-to-face interviews in the area and through the Internet. We employ a contingent valuation approach to assess the respondents' willingness to pay for the realisation of the defragmentation scenarios. It appears that the mean willingness to pay (WTP) for the two defragmentation scenarios is ¿ 162.2 (lognormal distribution) per respondent. Because the Veluwe is considered a nature park of national importance, we performed an aggregation of individual WTP estimates over Dutch households. With the resulting aggregate estimates we can compare the total costs and benefits of the two scenarios for habitat defragmentation in the Veluwe. In addition, we test whether respondents value the two scenarios equally. We also check whether the methods of data collection (face-to-face interviews and Internet questionnaires) have distinct influences on the stated WTP responses
    Is farther seed dispersal better? Spatial patterns of offspring mortality in three rainforest tree species with different dispersal abilities.
    Jansen, P.A. ; Bongers, F.J.J.M. ; Meer, P.J. van der - \ 2008
    Ecography 31 (2008)1. - ISSN 0906-7590 - p. 43 - 52.
    vouacapoua-americana caesalpiniaceae - french-guiana - tropical forests - virola-surinamensis - recruitment - survival - distance - seedlings - gaps - dynamics
    The paradigm that tropical trees with farther seed dispersal experience lower offspring mortality is currently based on within-species studies documenting higher survival of offspring located farther from conspecific adults and/or closer to light gaps. We determined whether the paradigm also holds among species by comparing spatial patterns of offspring mortality among three sympatric Neotropical rainforest tree species with the same seed dispersers but with different dispersal abilities. First, we assessed spatially non-random mortality for each species by measuring spatial shifts of the population recruitment curve (PRC) with respect to conspecific adults and light gaps across three early life stages: dispersed seeds, young seedlings and old seedlings. Then, we determined whether PRC shifts were greater for the species with short dispersal distances than for the species with greater dispersal distances. We found that the PRC shifted away from conspecific adults consistently across life stages, but we found no consistent PRC shifts towards gaps, suggesting that mortality was related more to the proximity of conspecifics than to absence of light gaps. PRC shifts away from adults were greatest in the species with the lowest dispersal ability, supporting the paradigm. Differential PRC shifts caused the spatial distribution of offspring to become almost independent with respect to adult trees and gaps in all three species, despite large differences in seed dispersal distance among these species. Our results provide direct empirical support for the paradigm that among tropical trees, species with farther seed dispersal are less impacted by spatially non-random mortality than are similar species with shorter dispersal distances. Thus, greater dispersal effectiveness merits extra investments of trees in seed dispersal ability, even at the cost of fecundity.
    Genetic population differentiation and connectivity among fragmented Moor frog (Rana arvalis) populations in The Netherlands
    Arens, P.F.P. ; Sluis, T. van der; Westende, W.P.C. van 't; Vosman, B. ; Vos, C.C. ; Smulders, M.J.M. - \ 2007
    Landscape Ecology 22 (2007)10. - ISSN 0921-2973 - p. 1489 - 1500.
    landscape genetics - flow - microsatellite - conservation - diversity - distance - markers - toad
    We studied the effects of landscape structure, habitat loss and fragmentation on genetic differentiation of Moor frog populations in two landscapes in The Netherlands (Drenthe and Noord-Brabant). Microsatellite data of eight loci showed small to moderate genetic differentiation among populations in both landscapes (F ST values 0.022 and 0.060, respectively). Both heterozygosity and population differentiation indicate a lower level of gene flow among populations in Noord-Brabant, where populations were further apart and have experienced a higher degree of fragmentation for a longer period of time as compared to populations in Drenthe. A significant isolation-by-distance pattern was found in Drenthe, indicating a limitation in dispersal among populations due to geographic distance. In Noord-Brabant a similar positive correlation was obtained only after the exclusion of a single long-time isolated population. After randomised exclusion of populations a significant additional negative effect of roads was found but not of other landscape elements. These results are discussed in view of improving methodology of assessing the effects of landscape elements on connectivity.
    Genetic diversity analysis using lowly polymorphic dominant markers: The example of AFLP in pigs.
    Foulley, J.L. ; Schriek, M. van; Groenen, M.A.M. ; Heuven, H.C.M. - \ 2006
    Journal of Heredity 97 (2006)3. - ISSN 0022-1503 - p. 244 - 252.
    dierveredeling - varkens - varkensrassen - rasverschillen - genetische diversiteit - genetische afstand - genetische analyse - genetische merkers - dna-fingerprinting - genfrequentie - dna-vermenigvuldiging - genetische polymorfie - genetische bronnen van diersoorten - aflp - animal breeding - pigs - pig breeds - breed differences - genetic diversity - genetic distance - genetic analysis - genetic markers - dna fingerprinting - gene frequency - dna amplification - genetic polymorphism - animal genetic resources - amplified fragment length polymorphism - population diversity - selective neutrality - distance - frequency
    DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F ST), and Reynolds genetic distances. A highly significant average FST of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of FST across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity
    Genetic diversity in European pigs utilizing amplified fragment lenght polymorphism markers. AFLP markers
    SanCristobal, M. ; Chevalet, C. ; Peleman, J. ; Heuven, H.C.M. ; Brugmans, B.W. ; Schriek, M. van; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. ; Amigues, Y. ; Boscher, M.Y. ; Russell, G. ; Law, A. ; Davoli, R. ; Russo, V. ; Desautes, C. ; Alderson, L. ; Fimland, E. ; Bagga, M. ; Delgado, J.V. ; Vega-Pla, J.L. ; Marinez, A.M. ; Ramos, M. ; Glodek, P. ; Meyer, J.N. ; Gandini, G.C. - \ 2006
    Animal Genetics 37 (2006)3. - ISSN 0268-9146 - p. 232 - 238.
    dierveredeling - varkens - varkensrassen - conservering - dna - allelen - genetische afstand - genetische diversiteit - genetische merkers - genotypen - heterozygotie - microsatellieten - wiskundige modellen - meishan - aflp - animal breeding - pigs - pig breeds - conservation - dna - alleles - genetic distance - genetic diversity - genetic markers - genotypes - heterozygosity - microsatellites - mathematical models - meishan - amplified fragment length polymorphism - population diversity - distance - trees - aflp
    The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3¿98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.
    Genetic diversity within and between European pig breeds using microsatellite markers
    SanCristobal, M. ; Chevalet, C. ; Haley, C.S. ; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. - \ 2006
    Animal Genetics 37 (2006)3. - ISSN 0268-9146 - p. 189 - 198.
    dierveredeling - varkens - wilde varkens - varkensrassen - conservering - rasverschillen - biodiversiteit - genetische afstand - genetische diversiteit - genetische merkers - heterozygotie - allelen - microsatellieten - populatiegenetica - statistische analyse - animal breeding - pigs - wild pigs - pig breeds - conservation - breed differences - biodiversity - genetic distance - genetic diversity - genetic markers - heterozygosity - alleles - microsatellites - population genetics - statistical analysis - populations - evolution - humans - loci - distance
    An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43–0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy–Weinberg expectations (P <0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright FST index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.
    An assessment of the European pig diversity using molecular markers: partitioning of diversity among breeds
    Ollivier, L. ; Alderson, L. ; Gandini, G.C. ; Foulley, J.L. ; Haley, C.S. ; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. - \ 2005
    Conservation Genetics 6 (2005)5. - ISSN 1566-0621 - p. 729 - 741.
    dierveredeling - varkens - varkensrassen - genetische diversiteit - genetische merkers - microsatellieten - moleculaire genetica - cryopreservering - kruising - conservering - uitsterven - rasverschillen - biodiversiteit - aflp - animal breeding - pigs - pig breeds - genetic diversity - genetic markers - microsatellites - molecular genetics - cryopreservation - crossbreds - conservation - extinction - breed differences - biodiversity - amplified fragment length polymorphism - subdivided populations - conservation genetics - livestock breeds - cattle breeds - management - distance - purposes - size
    Genetic diversity within and between breeds (and lines) of pigs was investigated. The sample comprised 68 European domestic breeds (and lines), including 29 local breeds, 18 varieties of major international breeds, namely Duroc, Hampshire, Landrace, Large White and Piétrain, and 21 commercial lines either purebred or synthetic, to which the Chinese Meishan and a sample of European wild pig were added. On average 46 animals per breed were sampled (range 12–68). The genetic markers were microsatellites (50 loci) and AFLP (amplified fragment length polymorphism, 148 loci). The analysis of diversity showed that the local breeds accounted for 56% of the total European between-breed microsatellite diversity, and slightly less for AFLP, followed by commercial lines and international breeds. Conversely, the group of international breeds contributed most to within-breed diversity, followed by commercial lines and local breeds. Individual breed contributions to the overall European between- and within-breed diversity were estimated. The range in between-breed diversity contributions among the 68 breeds was 0.04–3.94% for microsatellites and 0.24–2.94% for AFLP. The within-breed diversity contributions varied very little for both types of markers, but microsatellite contributions were negatively correlated with the between-breed contributions, so care is needed in balancing the two types of contribution when making conservation decisions. By taking into account the risks of extinction of the 29 local breeds, a cryopreservation potential (priority) was estimated for each of them.
    Comparison of three sampling methods in the characterization of cork oak stands for management purpose
    Paulo, M.J. ; Tomé, M. ; Otten, A. ; Stein, A. - \ 2005
    Canadian Journal of Forest Research 35 (2005)10. - ISSN 0045-5067 - p. 2295 - 2303.
    competition measures - predicting growth - point process - distance - trees
    The cork oak (Quercus suber L.) is an evergreen oak that has the ability to produce a continuous layer of cork tissue which regenerates after being removed. Cork oak stands can be diverse in structure. Young stands are often regularly spaced, whereas older stands usually show clustering and can be mixed with other species. Farmers assessing cork value use a zigzag sampling procedure within a stand. In this study we compare zigzag sampling with two other sampling methods, fixed-radius plot sampling and n-tree distance sampling, using a model for the costs of sampling. We used data from two cork oak stands in Portugal as well as data from six types of simulated stands. We found that zigzag is the poorest sampling method, as in most situations it produces estimators with larger bias and larger standard errors than that produced by the other two procedures. Fixed-radius plot sampling and n-tree distance sampling produce comparable results; however, fixed-radius plot sampling is preferred because it produces unbiased estimators
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