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.

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    Evolution of Hyaloperonospora effectors: ATR1 effector homologs from sister species of the downy mildew pathogen H. arabidopsidis are not recognised by RPP1WsB
    Solovyeva, I. ; Schmuker, A. ; Cano, L.M. ; Damme, M. van; Ploch, S. ; Kamoun, S. ; Thines, M. - \ 2015
    Mycological Progress 14 (2015). - ISSN 1617-416X - 9 p.
    plant immune-system - phylogenetic-relationships - peronospora-parasitica - oomycete effector - resistance gene - proteins - sequences - thaliana - reveals - plasmopara
    Like other plant-pathogenic oomycetes, downy mildew species of the genus Hyaloperonospora manipulate their hosts by secreting effector proteins. Despite intense research efforts devoted to deciphering the virulence and avirulence activities of effectors in the H. arabidopsidis/Arabidopsis thaliana pathosystem, there is only a single study in this pathosystem on the variation of effectors and resistance genes in natural populations, and the evolution of these effectors in the context of pathogen evolution is studied even less. In this work, the identification of A rabidopsis t haliana recognised (ATR)1-homologs is reported in two sister species of H. arabidopsidis, H. thlaspeos-perfoliati, and H. crispula, which are specialized on the host plants Microthlaspi perfoliatum and Reseda lutea, respectively. ATR1-diversity within these sister species of H. arabidopsidis was evaluated, and the ATR1-homologs from different isolates of H. thlaspeos-perfoliati and H. crispula were tested to see if they would be recognised by the previously characterised RPP1-WsB protein from A. thaliana. None of the effectors from the sister species was recognised, suggesting that due to the adaptation to altered or new targets after a host jump, features of variable effectors might vary to a degree that recognition of orthologous Avr-causing effectors is no longer effective and probably does not contribute to non-host immunity.
    Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]
    Khoury, C.K. ; Heider, B. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Miller, R.E. ; Scotland, R.W. ; Wood, J.R.I. ; Rossel, G. ; Eserman, L.A. ; Jarret, R.L. ; Yencho, G.C. ; Bernau, V. ; Juarez, H. ; Sotelo, S. ; Haan, S. de; Struik, P.C. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 14 p.
    species distribution models - phylogenetic-relationships - beta-carotene - convolvulaceae - sequences - diversity - evolution - bias - challenges - tolerance
    Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.
    Rhamphicarpa fistulosa, a widespread facultative hemi-parasitic weed, threatening rice production in Africa
    Rodenburg, J. ; Morawetz, J.J. ; Bastiaans, L. - \ 2015
    Weed Research 55 (2015). - ISSN 0043-1737 - p. 118 - 131.
    sub-saharan africa - fed lowland rice - phylogenetic-relationships - rhinanthus-minor - scrophulariaceae - vegetation - orobanchaceae - management - haustoria - habitats
    Rhamphicarpa fistulosa is a facultative hemi-parasitic plant of the Orobanchaceae family, adapted to wet soils. Apart from tropical Australia, it is only found in sub-Saharan Africa, where it is considered a minor weed in cereal crops such as rice. Due to this status, the species has received only sporadic attention. Recent field observations and encounters with rice farmers in several African countries showed that R. fistulosa is, however, a more serious and increasing production constraint than previously thought. Results from a systematic literature review and a global herbarium study support this. The species has a broad distribution over Africa (at least 35 countries from Madagascar to Senegal and from Sudan to South Africa) and a wide range in altitude (0–2150 m a.s.l.) and environment (waterlogged swamps to moist free-draining uplands). Rhamphicarpa fistulosa is relatively independent and persistent because of the presumably wide host range, the facultative nature of its parasitism and its prolific seed (estimated 100 000 seeds m-2 under moderate infestation levels). Finally, R. fistulosa causes severe yield losses (average 60%) and high regional annual economic losses (estimated US $175 million), while effective control options are scant and awareness of the species among important R&D stakeholders is almost absent. An integrated approach is advocated to assist the rice sector to reduce current R. fistulosa-inflicted losses and to prevent further spread of the species into new areas.
    Lineages in Nectriaceae: re-evaluating the generic status of Ilyonectria and allied genera
    Lombard, L. ; Merwe, N.A. Van Der; Groenewald, J.Z. ; Crous, P.W. - \ 2014
    Phytopathologia Mediterranea 53 (2014)3. - ISSN 0031-9465 - p. 515 - 532.
    black foot disease - cylindrocarpon-destructans - phylogenetic-relationships - multigene analysis - sp nov. - neonectria - rot - hypocreales - radicicola - grapevines
    Genera with cylindrocarpon-like asexual morphs are important pathogens of various herbaceous and woody plant hosts globally. Recent multi-gene studies of this generic complex indicated that the genus Ilyonectria is paraphyletic. The present study was therefore initiated to re-evaluate the generic status of Ilyonectria and at the same time address some taxonomic irregularities in the genera Cylindrodendrum and Neonectria. Using multi-gene DNA data and morphological comparisons, the genus Dactylonectria is introduced with 10 new combinations, several of which were previously treated in Ilyonectria. Two new species, D. hordeicola and D. pinicola, are also described. Furthermore, one new combination is provided in the genus Cylindrodendrum, and three new combinations in the genus Neonectria, for species previously treated in the genera Acremonium, Cylindrocarpon, Nectria and Neonectria. The aquatic genus Heliscus is reduced to synonymy under Neonectria.
    Ecogeographic variation in the morphology of two Asian wild rice species Oryza nivara and O. ruftipogon.
    Banaticla, M.C.N. ; Sosef, M.S.M. ; McNally, K.L. ; Sackville Hamilton, R. ; Berg, R.G. van den - \ 2013
    International Journal of Plant Sciences 174 (2013)6. - ISSN 1058-5893 - p. 896 - 909.
    genetic-structure - genus oryza - phylogenetic-relationships - evolutionary relationships - o-rufipogon - populations - diversity - perennis - sativa - differentiation
    To search for variation patterns and diagnostic features between Asian wild rice species, several numerical methods were applied to phenotypic data obtained from 116 accessions representing sympatric populations of Oryza nivara and Oryza rufipogon from tropical continental Asia and O. rufipogon populations from insular Southeast Asia and Australasia. Ordination and cluster analyses separate O. rufipogon from O. nivara, indicating the presence of two sympatric morphological species occupying different ecological niches. Oryza nivara and O. rufipogon are morphologically more differentiated in South Asia than in mainland Southeast Asia, implying more recent divergence and/or more interspecific gene flow among sympatric populations in the latter region. Oryza nivara exhibits South and Southeast Asian phenotypes while the Australasian populations of O. rufipogon appear as distinct from the rest of the species. Seedling height, culm number, and diameter; leaf length and width; and anther length were significantly correlated to certain geoclimatic factors and displayed contrasting correlation directions for O. nivara and O. rufipogon, implying that the two species respond differently to geographic and climatic gradients. Diagnostic characters are provided to delineate the species morphologically. The results suggest the strong influence of ecology on species morphology, existence of geographic races within species and morphological divergence between O. nivara and O. rufipogon.
    Alternaria redefined
    Woudenberg, J.H.C. ; Groenewald, J.Z. ; Binder, M. ; Crous, P.W. - \ 2013
    Studies in Mycology 75 (2013)1. - ISSN 0166-0616 - p. 171 - 212.
    ribosomal dna - phylogenetic-relationships - species-group - ulocladium - embellisia - genus - identification - sequences - taxonomy - nuclear
    Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species associated with a wide variety of substrates. In recent years, DNA-based studies revealed multiple non-monophyletic genera within the Alternaria complex, and Alternaria species clades that do not always correlate to species-groups based on morphological characteristics. The Alternaria complex currently comprises nine genera and eight Alternaria sections. The aim of this study was to delineate phylogenetic lineages within Alternaria and allied genera based on nucleotide sequence data of parts of the 18S nrDNA, 28S nrDNA, ITS, GAPDH, RPB2 and TEF1-alpha gene regions. Our data reveal a Pleospora/Stemphylium clade sister to Embellisia annulata, and a well-supported Alternaria clade. The Alternaria clade contains 24 internal clades and six monotypic lineages, the assemblage of which we recognise as Alternaria. This puts the genera Allewia, Brachycladium, Chalastospora, Chmelia, Crivellia, Embellisia, Lewia, Nimbya, Sinomyces, Teretispora, Ulocladium, Undifilum and Ybotromyces in synonymy with Alternaria. In this study, we treat the 24 internal clades in the Alternaria complex as sections, which is a continuation of a recent proposal for the taxonomic treatment of lineages in Alternaria. Embellisia annulata is synonymised with Dendryphiella salina, and together with Dendryphiella arenariae, are placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, which were previously associated with Alternaria, cluster within the Pleosporaceae, outside Alternaria s. str., whereas Alternariaster, a genus formerly seen as part of Alternaria, clusters within the Leptosphaeriaceae. Paradendryphiella is newly described, the generic circumscription of Alternaria is emended, and 32 new combinations and 10 new names are proposed. A further 10 names are resurrected, while descriptions are provided for 16 new Alternaria sections
    Tomato breeding in the genomics era: insights from a SNP array
    Víquez-Zamora, M. ; Vosman, B. ; Geest, H. van; Bovy, A.G. ; Visser, R.G.F. ; Finkers, H.J. ; Heusden, A.W. van - \ 2013
    BMC Genomics 14 (2013). - ISSN 1471-2164 - 28 p.
    backcross qtl analysis - phylogenetic-relationships - lycopersicon-hirsutum - evolutionary history - essential derivation - genus lycopersicon - l-pimpinellifolium - dna - construction - technologies
    Background - The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. Results - From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoesearlier results. Conclusions - Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome
    Phenotypic, Molecular, and Pathological Characterization of Colletotrichum acutatum Associated with Andean Lupine and Tamarillo in the Ecuadorian Andes
    Falconi, C. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2013
    Plant Disease 97 (2013)6. - ISSN 0191-2917 - p. 819 - 827.
    phytophthora-infestans - phylogenetic-relationships - olive anthracnose - ribosomal dna - sensu-lato - strawberry - identification - diversity - gloeosporioides - tomato
    Anthracnose is a serious problem of both Andean lupine and tamarillo in Ecuador. Morphological features, internal transcribed spacer (ITS) sequences, and host specificity were used to characterize Colletotrichum isolates from lupine and tamarillo. Based on phenotypic and molecular characterization, the causal agent of anthracnose on both hosts was Colletotrichum acutatum. All isolates were identified in a C. acutatum-specific polymerase chain reaction assay. Colony diameter, conidia shape, and insensitivity to benomyl also placed isolates from both hosts in the C. acutatum group. However, a detailed analysis of the ITS sequences placed the lupine and tamarillo isolates from the Ecuadorian Andean zone in two clades, with both lupine and tamarillo isolates in each clade. C. acutatum isolates from Andean lupine were distinct from other C. acutatum isolates on lupine around the world. In cross-infection studies, the diameter of lesions produced by isolates from each host was compared on the main stem of two tamarillo and three lupine cultivars. Some isolates produced larger lesions on the host from which they were isolated but others showed similar aggressiveness on their alternate host. Isolates from both hosts were biotrophic on lupine stems, producing little necrosis and abundant sporulation whereas, on tamarillo stems, they produced dark lesions with few conidia. The collection of C. acutatum isolates from lupine and tamarillo provides interesting material for the study quantitative host adaptation.
    Bat Rabies Surveillance in Europe
    Schatz, J. ; Fooks, A.R. ; McElhinney, L.M. ; Horton, D. ; Echevarria, J. ; Vázquez-Morón, S. ; Kooi, E.A. ; Rasmussen, T.B. ; Müller, T. ; Freuling, C. - \ 2013
    Zoonoses and Public Health 60 (2013)1. - ISSN 1863-1959 - p. 22 - 34.
    lyssavirus type-1 - serotine bats - phylogenetic-relationships - experimental-infection - eptesicus-serotinus - germany - origin - eblv-2 - populations - viruses
    Rabies is the oldest known zoonotic disease and was also the first recognized bat associated infection in humans. To date, four different lyssavirus species are the causative agents of rabies in European bats: the European Bat Lyssaviruses type 1 and 2 (EBLV-1, EBLV-2), the recently discovered putative new lyssavirus species Bokeloh Bat Lyssavirus (BBLV) and the West Caucasian Bat Virus (WCBV). Unlike in the new world, bat rabies cases in Europe are comparatively less frequent, possibly as a result of varying intensity of surveillance. Thus, the objective was to provide an assessment of the bat rabies surveillance data in Europe, taking both reported data to the WHO Rabies Bulletin Europe and published results into account. In Europe, 959 bat rabies cases were reported to the RBE in the time period 1977-2010 with the vast majority characterized as EBLV-1, frequently isolated in the Netherlands, North Germany, Denmark, Poland and also in parts of France and Spain. Most EBLV-2 isolates originated from the United Kingdom (UK) and the Netherlands, and EBLV-2 was also detected in Germany, Finland and Switzerland. Thus far, only one isolate of BBLV was found in Germany. Published passive bat rabies surveillance comprised testing of 28 of the 52 different European bat species for rabies. EBLV-1 was isolated exclusively from Serotine bats (Eptesicus serotinus and Eptesicus isabellinus), while EBLV-2 was detected in 14 Daubenton's bats (Myotis daubentonii) and 5 Pond bats (Myotis dasycneme). A virus from a single Natterer's bat (Myotis nattereri) was characterized as BBLV. During active surveillance, only oral swabs from 2 Daubenton's bats (EBLV-2) and from several Eptesicus bats (EBLV-1) yielded virus positive RNA. Virus neutralizing antibodies against lyssaviruses were detected in various European bat species from different countries, and its value and implications are discussed.
    Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed
    Herrero-Medrano, J. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. - \ 2013
    Animal Genetics 44 (2013)3. - ISSN 0268-9146 - p. 259 - 266.
    population-structure - phylogenetic-relationships - genetic diversity - dna - program - domestication - inference - software
    The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems – microsatellites, SNPs and mtDNA – were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (He = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm-based practices and farm-based breeding stocks can aid in the design of a sustainable breeding program for minority breeds.
    A Universal Microarray Detection Method for Identification of Multiple Phytophthora spp. Using Padlock Probes
    Sikora, K. ; Verstappen, E.C.P. ; Mendes, O. ; Schoen, C.D. ; Ristaino, J. ; Bonants, P.J.M. - \ 2012
    Phytopathology 102 (2012)6. - ISSN 0031-949X - p. 635 - 645.
    polymerase-chain-reaction - internal transcribed spacer - real-time pcr - ribosomal dna - phylogenetic-relationships - natural ecosystems - plant-pathogens - reaction assay - ramorum - quantification
    The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well-based microarray platform with colorimetric readout is used to detect and identify the different Phytophthora spp. PLPs are long oligonucleotides containing target complementary sequence regions at both their 5' and 3' ends which can be ligated on the target into a circular molecule. The ligation is point mutation specific; therefore, closely related sequences can be differentiated. This circular molecule can then be detected on a microarray. We developed 23 PLPs to economically important Phytophthora spp. based upon internal transcribed spacer-1 sequence differences between individual Phytophthora spp. Tests on genomic DNA of many Phytophthora isolates and DNA from environmental samples showed the specificity and utility of PLPs for Phytophthora diagnostics.
    How well do ITS rDNA sequences differentiate species of true morels (Morchella)?
    Du, X.H. ; Zhao, Q. ; Yang, Z.L. ; Hansen, K. ; Taskin, H. ; Büyükalaca, S. ; Dewsbury, D. ; Moncalvo, J.M. ; Douhan, G.W. ; Robert, V.A.R.G. ; Crous, P.W. ; Rehner, S.A. ; Rooney, A.P. ; Sink, S. ; O’Donnell, K. - \ 2012
    Mycologia 104 (2012)6. - ISSN 0027-5514 - p. 1351 - 1368.
    dna-sequences - phylogenetic-relationships - intragenomic variation - kingdom fungi - ribosomal dna - diversity - fusarium - identification - databases - recognition
    Arguably more mycophiles hunt true morels (Morchella) during their brief fruiting season each spring in the northern hemisphere than any other wild edible fungus. Concerns about overharvesting by individual collectors and commercial enterprises make it essential that science-based management practices and conservation policies are developed to ensure the sustainability of commercial harvests and to protect and preserve morel species diversity. Therefore, the primary objectives of the present study were to: (i) investigate the utility of the ITS rDNA locus for identifying Morchella species, using phylogenetic species previously inferred from multilocus DNA sequence data as a reference; and (ii) clarify insufficiently identified sequences and determine whether the named sequences in GenBank were identified correctly. To this end, we generated 553 Morchella ITS rDNA sequences and downloaded 312 additional ones generated by other researchers from GenBank using emerencia and analyzed them phylogenetically. Three major findings emerged: (i) ITS rDNA sequences were useful in identifying 48/62 (77.4%) of the known phylospecies; however, they failed to identify 12 of the 22 species within the species-rich Elata Subclade and two closely related species in the Esculenta Clade; (ii) at least 66% of the named Morchella sequences in GenBank are misidentified; and (iii) ITS rDNA sequences of up to six putatively novel Morchella species were represented in GenBank. Recognizing the need for a dedicated Web-accessible reference database to facilitate the rapid identification of known and novel species, we constructed Morchella MLST (, which can be queried with ITS rDNA sequences and those of the four other genes used in our prior multilocus molecular systematic studies of this charismatic genus.
    Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
    Schoch, C.L. ; Seifert, K.A. ; Huhndorf, S. ; Robert, V. ; Spouge, J.L. ; Levesque, C.A. ; Chen, W. ; Crous, P.W. ; Boekhout, T. ; Damm, U. ; Hoog, G.S. de; Eberhardt, U. ; Groenewald, J.Z. ; Groenewald, M. ; Hagen, F. ; Houbraken, J. ; Quaedvlieg, W. ; Stielow, B. ; Vu, T.D. ; Walther, G. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)16. - ISSN 0027-8424 - p. 6241 - 6246.
    arbuscular mycorrhizal fungi - phylogenetic-relationships - basidiomycetous yeasts - intragenomic variation - ectomycorrhizal fungi - species recognition - sequence-analysis - rpb1 sequences - rdna - subunit
    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
    Viral diseases of wild and farmed European eel Anguilla anguilla with particular reference to the Netherlands
    Beurden, S.J. van; Engelsma, M.Y. ; Roozenburg, I. ; Voorbergen-Laarman, H.A. ; Tulden, P.W. van; Kerkhoff, S. ; Nieuwstadt, A. ; Davidse, A. ; Haenen, O.L.M. - \ 2012
    Diseases of Aquatic Organisms 101 (2012). - ISSN 0177-5103 - p. 69 - 86.
    pancreatic necrosis virus - pillar cell necrosis - herpesvirus-anguillae - japanese eel - japonica temminck - phylogenetic-relationships - rhabdoviral dermatitis - taxonomic position - genome sequence - rainbow-trout
    Diseases are an important cause of losses and decreased production rates in freshwater eel farming, and have been suggested to play a contributory role in the worldwide decline in wild freshwater eel stocks. Three commonly detected pathogenic viruses of European eel Anguilla anguilla are the aquabirnavirus eel virus European (EVE), the rhabdovirus eel virus European X (EVEX), and the alloherpesvirus anguillid herpesvirus 1 (AngHV1). In general, all 3 viruses cause a nonspecific haemorrhagic disease with increased mortality rates. This review provides an overview of the current knowledge on the aetiology, prevalence, clinical signs and gross pathology of these 3 viruses. Reported experimental infections showed the temperature dependency and potential pathogenicity of these viruses for eels and other fish species. In addition to the published literature, an overview of the isolation of pathogenic viruses from wild and farmed A. anguilla in the Netherlands during the past 2 decades is given. A total of 249 wild A. anguilla, 39 batches of glass eels intended for farming purposes, and 239 batches of farmed European eels were necropsied and examined virologically. AngHV1 was isolated from wild A. anguilla yellow and silver eels from the Netherlands from 1998 until the present, while EVEX was only found sporadically, and EVE was never isolated. In farmed A. anguilla AngHV1 was also the most commonly isolated virus, followed by EVE and EVEX.
    Newcastle disease virus outbreaks: Vaccine mismatch or inadequate appication?
    Dortmans, J.C.F.M. ; Peeters, B.P.H. ; Koch, G. - \ 2012
    Veterinary Microbiology 160 (2012)1-2. - ISSN 0378-1135 - p. 17 - 22.
    shedding following vaccination - fusion protein - genotype vii - phylogenetic-relationships - molecular epidemiology - paramyxovirus type-1 - western-europe - china - chickens - strains
    Newcastle disease (ND) is one of the most important diseases of poultry, and may cause devastating losses in the poultry industry worldwide. Its causative agent is Newcastle disease virus (NDV), also known as avian paramyxovirus type 1. Many countries maintain a stringent vaccination policy against ND, but there are indications that ND outbreaks can still occur despite intensive vaccination. It has been argued that this may be due to antigenic divergence between the vaccine strains and circulating field strains. Here we present the complete genome sequence of a highly virulent genotype VII virus (NL/93) obtained from vaccinated poultry during an outbreak of ND in the Netherlands in 1992–1993. Using this strain, we investigated whether the identified genetic evolution of NDV is accompanied by antigenic evolution. In this study we show that a live vaccine that is antigenically adapted to match the genotype VII NL/93 outbreak strain does not provide increased protection compared to a classic genotype II live vaccine. When challenged with the NL/93 strain, chickens vaccinated with a classic vaccine were completely protected against clinical disease and mortality and virus shedding was significantly reduced, even with a supposedly suboptimal vaccine dose. These results suggest that it is not antigenic variation but rather poor flock immunity due to inadequate vaccination practices that may be responsible for outbreaks and spreading of virulent NDV field strains.
    Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks
    Kraus, R.H.S. ; Kerstens, H.H.D. ; Hooft, W.F. van; Megens, H.J.W.C. ; Elmberg, J. ; Tsvey, A. ; Sartakov, D. ; Soloviev, S.A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Ydenberg, R.C. ; Prins, H.H.T. - \ 2012
    BMC Evolutionary Biology 12 (2012). - ISSN 1471-2148 - 10 p.
    mallards anas-platyrhynchos - multilocus genotype data - linkage disequilibrium - population-structure - phylogenetic-relationships - hybridization patterns - finite population - miocene climate - waterfowl aves - average number
    The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct
    Ecology and Evolution of Soil Nematode Chemotaxis
    Rasmann, S. ; Ali, J.G. ; Helder, J. ; Putten, W.H. van der - \ 2012
    Journal of Chemical Ecology 38 (2012)6. - ISSN 0098-0331 - p. 615 - 628.
    plant-parasitic nematodes - root-feeding caterpillars - host search strategies - potato cyst nematodes - entomopathogenic nematodes - meloidogyne-incognita - natural enemies - c-elegans - phylogenetic-relationships - globodera-rostochiensis
    Plants influence the behavior of and modify community composition of soil-dwelling organisms through the exudation of organic molecules. Given the chemical complexity of the soil matrix, soil-dwelling organisms have evolved the ability to detect and respond to these cues for successful foraging. A key question is how specific these responses are and how they may evolve. Here, we review and discuss the ecology and evolution of chemotaxis of soil nematodes. Soil nematodes are a group of diverse functional and taxonomic types, which may reveal a variety of responses. We predicted that nematodes of different feeding guilds use host-specific cues for chemotaxis. However, the examination of a comprehensive nematode phylogeny revealed that distantly related nematodes, and nematodes from different feeding guilds, can exploit the same signals for positive orientation. Carbon dioxide (CO2), which is ubiquitous in soil and indicates biological activity, is widely used as such a cue. The use of the same signals by a variety of species and species groups suggests that parts of the chemo-sensory machinery have remained highly conserved during the radiation of nematodes. However, besides CO2, many other chemical compounds, belonging to different chemical classes, have been shown to induce chemotaxis in nematodes. Plants surrounded by a complex nematode community, including beneficial entomopathogenic nematodes, plant-parasitic nematodes, as well as microbial feeders, are thus under diffuse selection for producing specific molecules in the rhizosphere that maximize their fitness. However, it is largely unknown how selection may operate and how belowground signaling may evolve. Given the paucity of data for certain groups of nematodes, future work is needed to better understand the evolutionary mechanisms of communication between plant roots and soil biota
    The Phytophthora Genus Anno 2012
    Kroon, L.P.N.M. ; Brouwer, H. ; Cock, A.W.A.M. de; Govers, F. - \ 2012
    Phytopathology 102 (2012)4. - ISSN 0031-949X - p. 348 - 364.
    species causing root - high-temperature tolerant - sudden oak death - sp-nov. - western-australia - interspecific hybridization - phylogenetic-relationships - lithocarpus-densiflorus - heterothallic pathogen - molecular phylogeny
    Plant diseases caused by Phytophthora species will remain an ever increasing threat to agriculture and natural ecosystems. Phytophthora literally means plant destroyer, a name coined in the 19th century by Anton de Bary when he investigated the potato disease that set the stage for the Great Irish Famine. Phytophthora infestans, the causal agent of potato late blight, was the first species in a genus that at present has over 100 recognized members. In the last decade, the number of recognized Phytophthora species has nearly doubled and new species are added almost on a monthly basis. Here we present an overview of the 10 clades that are currently distinguished within the genus Phytophthora with special emphasis on new species that have been described since 1996 when Erwin and Ribeiro published the valuable monograph ‘Phytophthora diseases worldwide’ (35)
    Cylindrocarpon root rot: multi-gene analysis reveals novel species within the Ilyonectria radicicola species complex
    Cabral, A. ; Groenewald, J.Z. ; Rego, C. ; Oliveira, H. ; Crous, P.W. - \ 2012
    Mycological Progress 11 (2012)3. - ISSN 1617-416X - p. 655 - 688.
    black foot disease - phylogenetic-relationships - neonectria - anamorphs - fusarium - destructans - hypocreales - nectriaceae - ginseng - genera
    Ilyonectria radicicola and its Cylindrocarpon-like anamorph represent a species complex that is commonly associated with root rot disease symptoms on a range of hosts. During the course of this study, several species could be distinguished from I. radicicola sensu stricto based on morphological and culture characteristics. DNA sequence analysis of the partial ß-tubulin, histone H3, translation elongation factor 1-a and nuclear ribosomal RNA-Internal Transcribed Spacer (nrRNA-ITS) genes were employed to provide further support for the morphological species resolved among 68 isolates associated with root rot disease symptoms. Of the various loci screened, nrRNA-ITS sequences were the least informative, while histone H3 sequences were the most informative, resolving the same number of species as the combined dataset across the four genes. Within the Ilyonectria radicicola species complex, 12 new taxa are delineated occurring on a diverse range of hosts, the most common being Cyclamen, Lilium, Panax, Pseudotsuga, Quercus and Vitis.
    A taxonomic revision of the Neotropical poison frog genus Ranitomeya (Amphibia: Dendrobatidae)
    Brown, J.L. ; Twomey, E. ; Amézquita, A. ; Souza, M.B. ; Caldwell, J.P. ; Lötters, S. ; May, R. ; Melo-Sampaio, P.R. ; Mejía-Vargas, D. ; Perez-Peña, P. ; Pepper, M. ; Poelman, E.H. ; Sanchez-Rodriguez, M. ; Summers, K. - \ 2011
    Zootaxa 3083 (2011). - ISSN 1175-5326 - p. 1 - 120.
    mitochondrial-dna sequences - estimating bayes factors - parental care - phylogenetic-relationships - thermodynamic integration - genetic-divergence - tambopata region - biparental care - amazonian peru - evolution
    The Neotropical poison frog genus Ranitomeya is revised, resulting in one new genus, one new species, five synonymies and one species classified as nomen dubium. We present an expanded molecular phylogeny that contains 235 terminals, 104 of which are new to this study. Notable additions to this phylogeny include seven of the 12 species in the minuta group, 15 Ranitomeya amazonica, 20 R. lamasi, two R. sirensis, 30 R. ventrimaculata and seven R. uakarii. Previous researchers have long recognized two distinct, reciprocally monophyletic species groups contained within Ranitomeya, sensu Grant et al. 2006: the ventrimaculata group, which is distributed throughout much of the Amazon, and the minuta group of the northern Andes and Central America. We restrict Ranitomeya to the former group and erect a new genus, Andinobates Twomey, Brown, Amézquita & Mejía-Vargas gen. nov., for members of the minuta group. Other major taxonomic results of the current revision include the following: (i) A new species, Ranitomeya toraro Brown, Caldwell, Twomey, Melo-Sampaio & Souza sp. nov., is described from western Brazil. This species has long been referred to as R. ventrimaculata but new morphological and phylogenetic data place it sister to R. defleri. (ii) Examination of the holotype of R. ventrimaculata revealed that this specimen is in fact a member of what is currently referred to as R. duellmani, therefore, Dendrobates duellmani Schulte 1999 is considered herein a junior synonym of D. ventrimaculatus Shreve 1935 (= R. ventrimaculata). (iii) For the frogs that were being called R. ventrimaculata prior to this revision, the oldest available and therefore applicable name is R. variabilis. Whereas previous definitions of R. variabilis were restricted to spotted highland frogs near Tarapoto, Peru, our data suggest that this color morph is conspecific with lowland striped counterparts. Therefore, the definition of R. variabilis is greatly expanded to include most frogs which were (prior to this revision) referred to as R. ventrimaculata. (iv) Phylogenetic and bioacoustic evidence support the retention of R. amazonica as a valid species related to R. variabilis as defined in this paper. Based on phylogenetic data, R. amazonica appears to be distributed throughout much of the lower Amazon, as far east as French Guiana and the Amazon Delta and as far west as Iquitos, Peru. (v) Behavioral and morphological data, as well as phylogenetic data which includes topotypic material of R. sirensis and numerous samples of R. lamasi, suggest that the names sirensis, lamasi and biolat are applicable to a single, widespread species that displays considerable morphological variation throughout its range. The oldest available name for this group is sirensis Aichinger; therefore, we expand the definition of R. sirensis. (vi) Ranitomeya ignea and R. intermedia, elevated to the species status in a previous revision, are placed as junior synonyms of R. reticulata and R. imitator, respectively. (vii) Ranitomeya rubrocephala is designated as nomen dubium. In addition to taxonomic changes, this revision includes the following: (i) Explicit definitions of species groups that are consistent with our proposed taxonomy. (ii) A comprehensive dichotomous key for identification of ‘small’ aposematic poison frogs of South and Central America. (iii) Detailed distribution maps of all Ranitomeya species, including unpublished localities for most species. In some cases, these records result in substantial range extensions (e.g., R. uakarii, R. fantastica). (iv) Tadpole descriptions for R. amazonica, R. flavovittata, R. imitator, R. toraro sp. nov., R. uakarii and R. variabilis; plus a summary of tadpole morphological data for Andinobates and Ranitomeya species. (v) A summary of call data on most members of Andinobates and Ranitomeya, including call data of several species that have not been published before. (vi) A discussion on the continued impacts of the pet trade on poison frogs (vii) A discussion on several cases of potential Müllerian mimicry within the genus Ranitomeya. We also give opinions regarding the current debate on recent taxonomic changes and the use of the name Ranitomeya.
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