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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    Parametric estimation of P(X >Y) for normal distributions in the context of probabilistic environmental risk assessment.
    Jacobs, R. ; Bekker, A.A. ; Voet, H. van der; Braak, C.J.F. ter - \ 2015
    PeerJ 3 (2015). - ISSN 2167-8359
    species sensitivity distributions - stress-strength model - confidence-intervals - reliability - less - inference
    Estimating the risk, P(X > Y), in probabilistic environmental risk assessment of nanoparticles is a problem when confronted by potentially small risks and small sample sizes of the exposure concentration X and/or the effect concentration Y. This is illustrated in the motivating case study of aquatic risk assessment of nano-Ag. A non-parametric estimator based on data alone is not sufficient as it is limited by sample size. In this paper, we investigate the maximum gain possible when making strong parametric assumptions as opposed to making no parametric assumptions at all. We compare maximum likelihood and Bayesian estimators with the non-parametric estimator and study the influence of sample size and risk on the (interval) estimators via simulation. We found that the parametric estimators enable us to estimate and bound the risk for smaller sample sizes and small risks. Also, the Bayesian estimator outperforms the maximum likelihood estimators in terms of coverage and interval lengths and is, therefore, preferred in our motivating case study.
    Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
    Lohse, K. ; Frantz, L.A.F. - \ 2014
    Genetics 196 (2014)4. - ISSN 0016-6731 - p. 1241 - 1251.
    ancestral population sizes - dna-sequences - divergence - speciation - history - number - recombination - coalescent - migration - inference
    Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.
    Diaporthe species associated with Vaccinium, with specific reference to Europe
    Lombard, L. ; Leeuwen, G.C.M. van; Guarnaccia, V. ; Polizzi, G. ; Rijswick, P.C.J. van; Rosendahl, K.C.H.M. ; Gabler, J. ; Crous, P.W. - \ 2014
    Phytopathologia Mediterranea 53 (2014)2. - ISSN 0031-9465 - p. 287 - 299.
    phomopsis-vaccinii - maximum-likelihood - south-africa - stem canker - blueberry - grapevines - cranberry - australafricana - inference - diseases
    Species of the genus Vaccinium are commercially cultivated in Europe for their berries, which are highly valued for dietary and pharmaceutical properties. Cultivation is severely limited due to a range of fungal diseases, especially those caused by species of Diaporthe. A number of Diaporthe isolates have been collected from Vaccinium growing regions in Europe, and initially identified as D. vaccinii based on host association. Using DNA sequence inference of the combined ß-tubulin, calmodulin, translation elongation factor 1-alpha and the internal transcribed spacer region of the nuclear rDNA, along with morphological characteristics, six species were characterised. Diaporthe eres, D. vaccinii and D. viticola are known species and three novel taxa are described here as D. asheicola, D. baccae and D. sterilis. This study is the first confirmed report of D. vaccinii in Latvia and the Netherlands.
    Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
    Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Groenen, M. ; Lohse, H. - \ 2014
    Molecular Ecology 23 (2014)22. - ISSN 0962-1083 - p. 5566 - 5574.
    last glacial period - pig genomes - quaternary - evolution - reveals - domestication - demography - inference - sundaland - history
    In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology, 14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
    Measuring the impacts of production risk on technical efficiency: A state-contingent conditional order-m approach
    Serra, T. ; Oude Lansink, A.G.J.M. - \ 2014
    European Journal of Operational Research 239 (2014)1. - ISSN 0377-2217 - p. 237 - 242.
    nonparametric frontier models - cheap talk - technologies - uncertainty - inference - corn
    This article studies the influence of risk on farms' technical efficiency levels. The analysis extends the order-m efficiency scores approach proposed by Daraio and Simar (2005) to the state-contingent framework. The empirical application focuses on cross section data of Catalan specialized crop farms from the year 2011. Results suggest that accounting for production risks increases the technical performance. A 10% increase in output risk will result in a 2.5% increase in average firm technical performance. © 2014 Elsevier B.V. All rights reserved.
    Methods for cross--point analysis of double-demand functions in assessing animal preferences.
    Engel, B. ; Webb, L.E. ; Jensen, M.B. ; Reenen, C.G. van; Bokkers, E.A.M. - \ 2014
    Applied Animal Behaviour Science 160 (2014). - ISSN 0168-1591 - p. 138 - 147.
    different rooting materials - linear mixed models - motivation - likelihood - inference - pigs
    Cross point analysis of double demand functions provides a compelling way to quantify the strength of animal preferences for two simultaneously presented resources. During daily sessions, animals have to work to gain access to (a portion of) either resource, e.g. by pressing one of two panels a required number of times (the workload). Each panel is linked to one of the simultaneously presented resources. Workloads are varied over sessions and resources. Per session, for each resource the number of times that an animal is rewarded by access to the resource is observed. Four statistical approaches for analysis of these observations, including two novel approaches, are presented and discussed. The two novel approaches are based on relative numbers of rewards, i.e. analyses of proportions, while the other two methods that have been used before are based on absolute numbers of rewards, i.e. analyses of counts. Data from an experiment investigating preferences of Holstein-Friesian bull calves for two types of roughage (chopped and long hay) will be used to illustrate the calculations. The rationale of the four statistical approaches is given, and their pros and cons are discussed. The two novel approaches will be recommended for future practical use; they are directly tuned to the essential property of a double-demand experiment that animals have a choice between resources and consequently comprise considerably less population parameters than the other two approaches, allowing for more direct and clear interpretation. The novel approaches are less sensitive to model assumptions (more robust), and associated computer algorithms for fitting these models to the data are more reliable.
    Introducing Chaetothyriothecium, a new genus of Microthyriales
    Hongsanan, S. ; Chomnunti, P. ; Crous, P.W. ; Chukeatirote, E. ; Hyde, K.D. - \ 2014
    Phytotaxa 161 (2014)2. - ISSN 1179-3155 - p. 157 - 164.
    probability - sequences - bootstrap - inference - alignment - genera - trees - tools
    The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.
    New insights into domestication of carrot from root transcriptome analyses
    Rong, J. ; Lammers, Y. ; Strasburg, J.L. ; Schidlo, N.S. ; Ariyurek, Y. ; Jong, T.J. de; Klinkhamer, P.G.L. ; Smulders, M.J.M. ; Vrieling, K. - \ 2014
    BMC Genomics 15 (2014). - ISSN 1471-2164 - 15 p.
    daucus-carota l. - nucleotide polymorphism - wild - populations - inference - sativus - genome - diversity - sequences - selection
    Background - Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. Results - The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst =0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication. Conclusions - Western carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.
    Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
    Dam, J.C.J. van; Schaap, P.J. ; Martins dos Santos, V.A.P. ; Suarez Diez, M. - \ 2014
    BMC Systems Biology 8 (2014). - ISSN 1752-0509 - 21 p.
    data sets - expression profiles - microarray data - global analysis - biological data - promoter motif - inference - database - dormancy - regulon
    Background: Different methods have been developed to infer regulatory networks from heterogeneous omics datasets and to construct co-expression networks. Each algorithm produces different networks and efforts have been devoted to automatically integrate them into consensus sets. However each separate set has an intrinsic value that is diluted and partly lost when building a consensus network. Here we present a methodology to generate co-expression networks and, instead of a consensus network, we propose an integration framework where the different networks are kept and analysed with additional tools to efficiently combine the information extracted from each network. Results: We developed a workflow to efficiently analyse information generated by different inference and prediction methods. Our methodology relies on providing the user the means to simultaneously visualise and analyse the coexisting networks generated by different algorithms, heterogeneous datasets, and a suite of analysis tools. As a show case, we have analysed the gene co-expression networks of Mycobacterium tuberculosis generated using over 600 expression experiments. Regarding DNA damage repair, we identified SigC as a key control element, 12 new targets for LexA, an updated LexA binding motif, and a potential mismatch repair system. We expanded the DevR regulon with 27 genes while identifying 9 targets wrongly assigned to this regulon. We discovered 10 new genes linked to zinc uptake and a new regulatory mechanism for ZuR. The use of co-expression networks to perform system level analysis allows the development of custom made methodologies. As show cases we implemented a pipeline to integrate ChIP-seq data and another method to uncover multiple regulatory layers. Conclusions: Our workflow is based on representing the multiple types of information as network representations and presenting these networks in a synchronous framework that allows their simultaneous visualization while keeping specific associations from the different networks. By simultaneously exploring these networks and metadata, we gained insights into regulatory mechanisms in M. tuberculosis that could not be obtained through the separate analysis of each data type.
    Phylogenetics, ancestral state reconstruction, and a new infrafamilial classification of the pantropical Ochnaceae (Medusagynaceae, Ochnaceae s.str., Quiinaceae) based on five DNA regions
    Schneider, J.V. ; Bissiengou, P. ; Amaral, M.D. ; Tahir, A. ; Fay, M.F. ; Thines, M. ; Sosef, M.S.M. ; Zizka, G. ; Chatrou, L.W. - \ 2014
    Molecular Phylogenetics and Evolution 78 (2014)20. - ISSN 1055-7903 - p. 199 - 214.
    chain monte-carlo - angiosperm phylogeny - venezuelan guayana - matk sequences - malpighiales - evolution - morphology - inference - systematics - taxa
    Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia and Perissocarpa and DNA sequence data for five DNA regions (ITS, matK, ndhF, rbcL, trnL-F), we provide for the first time a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogenetic backbone of the family. Based on this, we present a new classification of Ochnaceae s.l., with Medusagynoideae and Quiinoideae included as subfamilies and the former subfamilies Ochnoideae and Sauvagesioideae recognized at the rank of tribe. Our data support a monophyletic Ochneae, but Sauvagesieae in the traditional circumscription is paraphyletic because Testulea emerges as sister to the rest of Ochnoideae, and the next clade shows Luxemburgia+Philacra as sister group to the remaining Ochnoideae. To avoid paraphyly, we classify Luxemburgieae and Testuleeae as new tribes. The African genus Lophira, which has switched between subfamilies (here tribes) in past classifications, emerges as sister to all other Ochneae. Thus, endosperm-free seeds and ovules with partly to completely united integuments (resulting in an apparently single integument) are characters that unite all members of that tribe. The relationships within its largest clade, Ochnineae (former Ochneae), are poorly resolved, but former Ochninae (Brackenridgea, Ochna) are polyphyletic. Within Sauvagesieae, the genus Sauvagesia in its broad circumscription is polyphyletic as Sauvagesia serrata is sister to a clade of Adenarake, Sauvagesia spp., and three other genera. Within Quiinoideae, in contrast to former phylogenetic hypotheses, Lacunaria and Touroulia form a clade that is sister to Quiina. Bayesian ancestral state reconstructions showed that zygomorphic flowers with adaptations to buzz-pollination (poricidal anthers), a syncarpous gynoecium (a near-apocarpous gynoecium evolved independently in Quiinoideae and Ochninae), numerous ovules, septicidal capsules, and winged seeds with endosperm are the ancestral condition in Ochnoideae. Although in some lineages poricidal anthers were lost secondarily, the evolution of poricidal superstructures secured the maintenance of buzz-pollination in some of these genera, indicating a strong selective pressure on keeping that specialized pollination system.
    Inferring the Gene Network Underlying the Branching of Tomato Inflorescence
    Astola, L. ; Stigter, J.D. ; Dijk, A.D.J. van; Daelen, R. van; Molenaar, J. - \ 2014
    PLoS ONE 9 (2014)4. - ISSN 1932-6203 - 7 p.
    flowering time - reproductive structure - regulatory networks - abscission zone - inference - meristem - lycopersicon - falsiflora - jointless
    The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior
    Risk factors associated with health disorders in sport and leisure horses in The Netherlands
    Visser, E.K. ; Neijenhuis, F. ; Graaf-Roelfsema, E. de; Wesselink, H.G.M. ; Boer, J. de; Wijhe-Kiezebrink, M.C. van; Engel, B. ; Reenen, C.G. van - \ 2014
    Journal of Animal Science 92 (2014)2. - ISSN 0021-8812 - p. 844 - 855.
    respiratory-disease - insulin-resistance - part 1 - prevalence - management - obesity - welfare - laminitis - inference - responses
    Horses are used for a wide variety of purposes from being used for recreational purposes to competing at an international level. With these different uses, horses have to adapt to numerous challenges and changes in their environment, which can be a challenge itself in continuously safeguarding their welfare. The objective of this study was to assess the prevalence of health disorders with clinical examination and identify possible risk factors of health disorders affecting horse welfare in professional husbandry systems in the Netherlands. With the use of fixed protocols for recording health aspects in horses, 150 horse farms voluntarily participating in the study were assessed by trained assessors. On each farm, 20 horses were clinically examined, in total almost 3,000 animals. This study recorded on the basis of the clinical examinations: the respiratory system (i.e., abnormal breathing [1%], coughing [1%], nasal discharge [1.9%]), body condition (i.e., 18.8% fat body condition and 6.4% poor body condition), locomotion (14.5% exhibited irregularity of locomotion and 4.8% were lame), back palpation (a light response [22.6%] and moderate to severe response [8.4%]), mouth (i.e., irregularities on mouth corners [3.4%] and bars [3.4%]), and ocular discharge (12%). Risk factor analysis, stepwise using mixed model regression, demonstrated several risk factors for health aspects. Horses used for instruction (riding lessons) were almost two times more at risk to develop moderate to severe back pain compared to horses used for recreation (odds ratios [OR] = 0.54) or for competition (OR = 0.61). Horses used for instruction (riding school lessons), breeding, or recreation all had a higher risk for irregular locomotion or lameness compared to competition horses (OR = 0.42, OR = 0.55, OR = 2.14, respectively). Horses used for recreation were more prone to have a higher BCS compared to horses used for breeding (OR = 3.07) and instruction (OR = 2.06). The prevalence of health problems and the identified risk factors are valid for the horses in the present study in which farms voluntarily participated. Furthermore, the results may provide the basis for horse welfare and health programs on farm and horse industry levels. With the development of a valid welfare monitoring system for the horse industry, the welfare of horses can be increased through improving awareness and stimulating changes in management.
    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.
    Government interventions and default risk: Does one size fit all?
    Klomp, J.G. - \ 2013
    Journal of Financial Stability 9 (2013)4. - ISSN 1572-3089 - p. 641 - 653.
    quantile regression - interest-rates - inference - crisis
    We examine the effectiveness of the financial sector rescue packages provided by the national governments during the 2008 financial crisis. This study questions the implicit assumption that government interventions have an uniform effect on the default risk of individual banks. After testing the results for sensitivity, our main findings suggest that there exists a significant negative relationship between the announcement of the financial sector rescue packages and the daily change of the credit default premium. However, quantile regressions show that the effectiveness of these packages differs across banks: most interventions do not decrease the risk of intermediate to low-risk banks, while they do reduce the risk of high-risk banks. Besides, we find that interventions aimed at specific financial institutions are more effective in restraining banking risk than broad interventions taken to stabilize the financial market as a whole.
    Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies
    Pham, H.T.M. ; Berthouly-Salazar, C. ; Crooijmans, R.P.M.A. - \ 2013
    Animal Genetics 44 (2013)5. - ISSN 0268-9146 - p. 509 - 521.
    multilocus genotype data - breeds - program - microsatellites - construction - resources - inference - software - ecotypes - alleles
    The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20 microsatellites. Consequently, the VNN populations exhibited a higher diversity than did CNO populations in terms of number of alleles but showed a slightly lower observed heterozygosity. The VNN populations showed in total seven private alleles, whereas no CNO private alleles were found. The expected heterozygosity of 0.576 in the VNN populations was higher than the observed heterozygosity of 0.490, leading to heterozygote deficiency within populations. This issue could be partly explained by the Wahlund effect due to fragmentation of several populations between chicken flocks. Molecular analysis of variance showed that most of genetic variation was found within VNN populations. The Bayesian clustering analysis showed that VNN and CNO chickens were separated into two distinct groups with little evidence for gene flow between them. Among the 24 populations, 13 were successfully assigned to their own cluster, whereas the structuring was not clear for the remaining 11 chicken populations. The contributions of 24 populations to the total genetic diversity were mostly consistent across two approaches, taking into account the within- and between-populations genetic diversity and allelic richness. The black H'mong, Lien Minh, Luong Phuong and Red Jungle Fowl were ranked with the highest priorities for conservation according to Caballero and Toro's and Petit's approaches. In conclusion, a national strategy needs to be set up for Vietnamese chicken populations, with three main components: conservation of high-priority breeds, within-breed management with animal exchanges between flocks to avoid Wahlund effect and monitoring of inbreeding rate.
    Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
    Frantz, L.A.F. ; Madsen, O. ; Megens, H.J.W.C. ; Paudel, Y. ; Bosse, M. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Schraiber, J.G. - \ 2013
    Genome Biology 14 (2013)9. - ISSN 1474-7596 - 12 p.
    last glacial period - southeast-asia - recombination rates - complex speciation - maximum-likelihood - genetic-evidence - se asia - evolution - inference - reconstructions
    Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.
    Sodiomyces alkalinus, a new holomorphic alkaliphilic ascomycete within the Plectoshaerellaceae
    Grum-Grzhimaylo, A. ; Debets, A.J.M. ; Diepeningen, A.D. van; Georgieva, M.L. ; Bilanenko, E.N. - \ 2013
    Persoonia 31 (2013). - ISSN 0031-5850 - p. 147 - 158.
    classification - inference - trees - fungi
    In this study we reassess the taxonomic reference of the previously described holomorphic alkaliphilic fungus Heleococcum alkalinum isolated from soda soils in Russia, Mongolia and Tanzania. We show that it is not an actual member of the genus Heleococcum (order Hypocreales) as stated before and should, therefore, be excluded from it and renamed. Multi-locus gene phylogeny analyses (based on nuclear ITS, 5.8S rDNA, 28S rDNA, 18S rDNA, RPB2 and TEF1-alpha) have displayed this fungus as a new taxon at the genus level within the family Plectosphaerellaceae, Hypocreomycetidae, Ascomycota. The reference species of actual Heleococcum members showed clear divergence from the strongly supported Heleococcum alkalinum position within the Plectosphaerellaceae, sister to the family Glomerellaceae. Eighteen strains isolated from soda lakes around the world show remarkable genetic similarity promoting speculations on their possible evolution in harsh alkaline environments. We established the pH growth optimum of this alkaliphilic fungus at c. pH 10 and tested growth on 30 carbon sources at pH 7 and 10. The new genus and species, Sodiomyces alkalinus gen. nov. comb. nov., is the second holomorphic fungus known within the family, the first one being Plectosphaerella – some members of this genus are known to be alkalitolerant. We propose the Plectosphaerellaceae family to be the source of alkaliphilic filamentous fungi as also the species known as Acremonium alcalophilum belongs to this group
    Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle
    Hulsegge, B. ; Calus, M.P.L. ; Windig, J.J. ; Hoving, A.H. ; Maurice - Van Eijndhoven, M.H.T. ; Hiemstra, S.J. - \ 2013
    Journal of Animal Science 91 (2013)11. - ISSN 0021-8812 - p. 5128 - 5134.
    single-nucleotide polymorphisms - population divergence - informative markers - assignment - ancestry - individuals - inference - holstein - jersey - phase
    Reliable breed assignment can be performed with SNP. Currently, high density SNP chips are available with large numbers of SNP from which the most informative SNP can be selected for breed assignment. Several methods have been published to select the most informative SNP to distinguish among breeds. In this study, we evaluated Delta, Wright's FST, and Weir and Cockerham's FST, and extended these methods by adding a rule to avoid selection of sets of SNP in high linkage disequilibrium (LD) providing the same information. The SNP that had a r2 value>0.3 with any of the SNP already selected were discarded. The different selection methods were evaluated for both the 50K SNP and 777K Bovine BeadChip. Animals from 4 cattle breeds (989 Holstein Friesian, 97 Groningen White headed, 137 Meuse-Rhine-Yssel, and 64 Dutch Friesian) were genotyped. After editing 30,447 and 452,525 SNP were available for the 50K and 777K SNP chip, respectively. All selection methods showed that only a small set of SNP is needed to differentiate among the 4 Dutch cattle breeds, whereas comparison of the selection methods showed only small differences. In general, the 777K performed marginally better than the 50K BeadChip, especially at higher confidence thresholds. The rule to avoid selection of SNP in high LD reduced the required number of SNP to achieve correct breed assignment. The Global Weir and Cockerham's FST performed marginally better than other selection methods. There was little overlap in the SNP selected from the 2 BeadChips, whereas the number of SNP selected was about the same.
    Reappraisal of the genus Alternariaster (Dothideomycetes)
    Alves, J.L. ; Woudenberg, J.H.C. ; Duarte, L.L. ; Crous, P.W. ; Barreto, R.W. - \ 2013
    Persoonia 31 (2013). - ISSN 0031-5850 - p. 77 - 85.
    inference - mrbayes - brazil
    Alternariaster was erected in 2007 to accommodate Alternaria helianthi, a fungal species known to cause leaf spots on Helianthus annuus (sunflower). It was segregated from Alternaria based on conidial morphology. Recently an unknown alternaria-like dematiaceous fungus was found associated with leaf spots on Bidens sulphurea (yellow cosmos) in Brazil. Based on a multi-gene phylogeny of parts of the ITS and LSU genes, this fungus was placed within the Leptosphaeriaceae with Alternariaster helianthi as its closest neighbour. Additional genes sequenced, RPB2 and GAPDH, confirmed this close relationship. The fungus on B. sulphurea has smaller conidia, 50¿97.5 × 12.5¿20 µm, compared to Al. helianthi, 80¿160 × 18¿30 µm, and lacks oblique or transverse septa which can be present in Al. helianthi. Pathogenicity studies on 18 plant species belonging to the Compositae showed that the B. sulphurea fungus only infected B. sulphurea, whereas Al. helianthi infected H. annuus and Galinsoga quadriradiata, a yet unreported host of Al. helianthi. The fungus causing disease on B. sulphurea is hence closely related but phylogenetically, morphologically and pathologically distinct from Al. helianthi, and therefore newly described as Alternariaster bidentis. The collection of a second species in the genus Alternariaster and the multigene phylogenetic analysis of these two species, confirmed Alternariaster to be a well-delimited genus in the Leptosphaeriaceae rather than the Pleosporaceae, to which Alternaria belongs
    First worldwide UNEP interlaboratory study on persistent organic pollutants (POPs) with data on polychlorinated biphenyls and organochlorine pesticides
    Leeuwen, S.P.J. van; Bavel, B. van; Boer, J. de - \ 2013
    TrAC : Trends in Analytical Chemistry 46 (2013). - ISSN 0165-9936 - p. 110 - 117.
    quasimeme laboratory performance - population characteristics - petroleum-hydrocarbons - new-model - uncertainties - environment - inference - fish
    The first worldwide interlaboratory study on persistent organic pollutants (POPs) under the Stockholm Convention was organized, with a participation of 103 laboratories from Asia, Europe, the Americas, Africa and Australia, of which the majority submitted data on polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs). The participating laboratories were requested to analyze different matrices (i.e. two test solutions, and test materials for fish, sediment, fly ash and human milk). All results were statistically evaluated according to the procedures used in the European Union-based QUASIMEME proficiency-testing scheme
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