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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Phylogenetic analysis of highly pathogenic avian influenza A (H5N8) virus outbreak strains provides evidence for four separate introductions and one between-poultry farm transmission in the Netherlands, November 2014
Bouwstra, R.J. ; Koch, G. ; Heutink, C.G. ; Harders, F.L. ; Spek, A. van der; Elbers, A.R.W. ; Bossers, A. - \ 2015
EuroSurveillance 20 (2015)26. - ISSN 1025-496X
mitochondrial-dna - a viruses - sequence - amplification - china - h5
Phylogenetic analysis of highly pathogenic avian influenza A(H5N8) virus strains causing outbreaks in Dutch poultry farms in 2014 provides evidence for separate introduction of the virus in four outbreaks in farms located 16–112 km from each other and for between-farm transmission between the third and fourth outbreak in farms located 550 m from each other. In addition, the analysis showed that all European and two Japanese H5N8 virus strains are very closely related and seem to originate from a calculated common ancestor, which arose between July and September 2014. Our findings suggest that the Dutch outbreak virus strain ‘Ter Aar’ and the first German outbreak strain from 2014 shared a common ancestor. In addition, the data indicate that the Dutch outbreak viruses descended from an H5N8 virus that circulated around 2009 in Asia, possibly China, and subsequently spread to South Korea and Japan and finally also to Europe. Evolution of the virus seemed to follow a parallel track in Japan and Europe, which supports the hypothesis that H5N8 virus was exchanged between migratory wild waterfowl at their breeding grounds in Siberia and from there was carried by migrating waterfowl to Europe.
Phyllosticta species on citrus: Risk estimation of resistance to QoI fungicides and identification of species with cytochrome b gene sequences
Stammler, G. ; Schutte, G.C. ; Speakman, J. ; Miessner, S. ; Crous, P.W. - \ 2013
Crop Protection 48 (2013). - ISSN 0261-2194 - p. 6 - 12.
guignardia-citricarpa - black spot - botrytis-cinerea - south-africa - mitochondrial-dna - pyrenophora-teres - valencia oranges - f129l mutation - causal agent - mangiferae
Isolates of three fungal species associated with citrus, Phyllosticta citricarpa, Phyllosticta citriasiana and Phyllosticta capitalensis, collected from different citrus growing countries of the world, were investigated for their sensitivities to the QoI fungicides pyraclostrobin and azoxystrobin. Isolates were highly sensitive in microtiter tests and EC50 values were in narrow ranges, which indicate no acquired adaptation to QoIs. The resistance risk of P. citricarpa to QoIs is considered low since an intron was found immediately after codon 143 in the cytochrome b gene. The presence of an intron is known to reduce the risk of the G143A mutation, the mutation which causes QoI resistance with high resistance factors. The other two species had no intron and therefore are considered having a higher resistance risk. Impact of these two species is rather low, since P. citriasiana is restricted in its regional and host distribution and P. capitalensis is non-pathogenic. Furthermore, the development of a rapid and reliable assay for species detection and identification was made possible based on an analysis of the cytochrome b gene.
Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms
Kraus, R.H.S. ; Hooft, W.F. van; Megens, H.J.W.C. ; Tsvey, A. ; Fokin, S.Y. ; Ydenberg, R.C. ; Prins, H.H.T. - \ 2013
Molecular Ecology 22 (2013)1. - ISSN 0962-1083 - p. 41 - 55.
maximum-likelihood-estimation - mallard anas-platyrhynchos - influenza-a viruses - population-structure - mitochondrial-dna - phylogenetic networks - coalescent approach - genetic-structure - biased dispersal - white sharks
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.
DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods
Velzen, R. van; Weitschek, E. ; Felici, G. ; Bakker, F.T. - \ 2012
PLoS One 7 (2012)1. - ISSN 1932-6203 - 12 p.
mitochondrial-dna - phylogenetic trees - molecular markers - sequence data - identification - diptera - fish - diversity - selection - taxonomy
Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a ‘barcode gap’ and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (~75%) than for older species (~97%) (P
Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci
Andre, C. ; Larsson, L.C. ; Laikre, L. ; Bekkevold, D. ; Brigham, J. ; Carvalho, G.R. ; Dahlgren, T.G. ; Hutchinson, W.F. ; Mariani, S. ; Mudde, C.M. ; Ruzzante, D.E. ; Ryman, N. - \ 2011
Heredity 106 (2011)2. - ISSN 0018-067X - p. 270 - 280.
cod gadus-morhua - salmon salmo-salar - histocompatibility class-i - mitochondrial-dna - north-sea - molecular markers - balancing selection - statistical power - natural-selection - computer-program
In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species. Heredity (2011) 106, 270-280; doi:10.1038/hdy.2010.71; published online 16 June 2010
Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in south Africa
Bastos, A.D.S. ; Nair, D. ; Taylor, P.J. ; Brettschneider, H. ; Kirsten, F. ; Mostert, E. ; Maltitz, E. ; Lamb, J.M. ; Hooft, W.F. van; Belmain, S.R. ; Contrafatto, G. ; Downs, S. ; Chimimba, C.T. - \ 2011
BMC Genetics 12 (2011). - ISSN 1471-2156 - 18 p.
mitochondrial-dna - native-range - black rats - prediction - rodentia - muridae - colonization - phylogenies - madagascar - radiation
Background: South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present.Results: To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species.Conclusions: This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.
Calorie restriction causes healthy life span extension in the filamentous fungus Podospora anserina
Diepeningen, A.D. van; Maas, M.F.P.M. ; Huberts, D.H.E.W. ; Goedbloed, D.J. ; Engelmoer, D.J.P. ; Slakhorst, S.M. ; Koopmanschap, A.B. ; Krause, F. ; Dencher, N.A. ; Sellem, C.H. ; Sainsard-Chanet, A. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2010
Mechanisms of Ageing and Development 131 (2010)1. - ISSN 0047-6374 - p. 60 - 68.
respiratory-chain supercomplexes - cytochrome-c-oxidase - group-ii introns - saccharomyces-cerevisiae - supramolecular organization - mitochondrial-dna - senescence - dynamics
Although most fungi appear to be immortal, some show systemic senescence within a distinct time frame. Podospora anserina for example shows an irreversible growth arrest within weeks of culturing associated with a destabilization of the mitochondrial genome. Here, we show that calorie restriction (CR), a regimen of under-nutrition without malnutrition, increases not only life span but also forestalls the aging-related decline in fertility. Similar to respiratory chain deficiencies the life span extension is associated with lower levels of intracellular H2O2 measurements and a stabilization of the mitochondrial genome. Unlike respiratory chain deficiencies, CR cultures have a wild-type-like OXPHOS machinery similar to that of well-fed cultures as shown by native electrophoresis of mitochondrial protein complexes. Together, these data indicate that life span extension via CR is fundamentally different from that via respiratory chain mutations: Whereas the latter can be seen as a pathology, the former promotes healthy life span extension and may be an adaptive response
Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates
Chiari, Y. ; Meijden, A. van der; Madsen, O. ; Vences, M. ; Meyer, A. - \ 2009
Frontiers in Zoology 6 (2009). - ISSN 1742-9994 - 15 p.
nuclear rag-1 gene - v(d)j recombination - mitochondrial-dna - evolution - sequences - diversification - patterns - frogs - amphibians - inference
Background: The Recombination Activating Proteins, RAG1 and RAG2, play a crucial role in the immune response in vertebrates. Among the nuclear markers currently used for phylogenetic purposes, Rag1 has especially enjoyed enormous popularity, since it successfully contributed to elucidating the relationships among and within a large variety of vertebrate lineages. We here report on a comparative investigation of the genetic variation, base composition, presence of indels, and selection in Rag1 in different vertebrate lineages (Actinopterygii, Amphibia, Aves, Chondrichthyes, Crocodylia, Lepidosauria, Mammalia, and Testudines) through the analysis of 582 sequences obtained from Genbank. We also analyze possible differences between distinct parts of the gene with different type of protein functions. Results: In the vertebrate lineages studied, Rag1 is over 3 kb long. We observed a high level of heterogeneity in base composition at the 3(rd) codon position in some of the studied vertebrate lineages and in some specific taxa. This result is also paralleled by taxonomic differences in the GC content at the same codon position. Moreover, positive selection occurs at some sites in Aves, Lepidosauria and Testudines. Indels, which are often used as phylogenetic characters, are more informative across vertebrates in the 5' than in the 3'-end of the gene. When the entire gene is considered, the use of indels as phylogenetic character only recovers one major vertebrate clade, the Actinopterygii. However, in numerous cases insertions or deletions are specific to a monophyletic group. Conclusions: Rag1 is a phylogenetic marker of undoubted quality. Our study points to the need of carrying out a preliminary investigation on the base composition and the possible existence of sites under selection of this gene within the groups studied to avoid misleading resolution. The gene shows highly heterogeneous base composition, which affects some taxa in particular and contains sites under positive selection in some vertebrate lineages in the 5'-end. The first part of the gene (5'-end) is more variable than the second (3'-end), and less affected by a heterogeneous base composition. However, in some vertebrate lineages the 5'-end of the gene is not yet widely used for phylogenetic studies
Allopatric origin of cryptic butterfly species that were discovered feeding on distinct host plants in sympatry.
McBride, L.C. ; Velzen, R. van; Larsen, T.B. - \ 2009
Molecular Ecology 18 (2009)17. - ISSN 0962-1083 - p. 3639 - 3651.
parasitoid flies diptera - dna barcodes - mitochondrial-dna - reproductive isolation - astraptes-fulgerator - phytophagous insects - speciation - evolution - lepidoptera - divergence
Surveys of tropical insects are increasingly uncovering cryptic species ¿ morphologically similar yet reproductively isolated taxa once thought to comprise a single interbreeding entity. The vast majority of such species are described from a single location. This leaves us with little information on geographic range and intraspecific variation and limits our ability to infer the forces responsible for generating such diversity. For example, in herbivorous and parasitic insects, multiple specialists are often discovered within what were thought to be single more generalized species. Host shifts are likely to have contributed to speciation in these cases. But when and where did those shifts occur, and were they facilitated by geographic isolation? We attempted to answer these questions for two cryptic species within the butterfly Cymothoe egesta that were recently discovered on different host plants in central Cameroon. We first used mtDNA markers to separate individuals collected on the two hosts within Cameroon and then extended our analysis to incorporate individuals collected across the entire pan-Afrotropical range of the original taxon. To our surprise, we found that the species are almost entirely allopatric, dividing the original range and overlapping only in the narrow zone of West-Central Africa where they were first discovered in sympatry. This finding, combined with analyses of genetic variation within each butterfly species, strongly suggests that speciation occurred in allopatry, probably during the Pleistocene. We discuss the implications of our results for understanding speciation among other cryptic species recently discovered in the tropics and argue that more work is needed on geographic patterns and host usage in such taxa
Origins of asexuality in Bryobia mites (Acari: Tetranychidae)
Ros, V.I.D. ; Breeuwer, J.A.J. ; Menken, S.B.J. - \ 2008
BMC Evolutionary Biology 8 (2008). - ISSN 1471-2148 - 16 p.
wolbachia-induced parthenogenesis - oxidase subunit-i - leptopilina-clavipes hymenoptera - drosophila-simulans - mitochondrial-dna - phylogenetic-relationships - muscidifurax-uniraptor - bdelloid rotifers - spider-mite - sex
Background Obligate asexual reproduction is rare in the animal kingdom. Generally, asexuals are considered evolutionary dead ends that are unable to radiate. The phytophagous mite genus Bryobia contains a large number of asexual species. In this study, we investigate the origin and evolution of asexuality using samples from 111 populations in Europe, South Africa and the United States, belonging to eleven Bryobia species. We also examine intraspecific clonal diversity for one species, B. kissophila, by genotyping individuals from 61 different populations. Knowledge on the origin of asexuality and on clonal diversity can contribute to our understanding of the paradox of sex. Results The majority (94%) of 111 sampled populations reproduces asexually. Analysis of part of nuclear 28S rDNA shows that these asexuals do not form a monophyletic clade. Analysis of the mitochondrial COI region shows that intraspecific variation is extensive (up to 8.8%). Within B. kissophila, distinct clades are found, which are absent at the nuclear 28S rDNA level. Moreover, paraphyletic patterns are found at the mitochondrial DNA. Conclusion Asexuality is widespread in the genus Bryobia, signifying that some animal taxa do contain a high number of asexuals. We argue that asexuality originated multiple times within Bryobia. Wolbachia bacteria cause asexuality in at least two Bryobia species and may have infected different species independently. The high intraspecific clonal diversity and the patterns of paraphyly at the mitochondrial DNA in B. kissophila might be explained by a high mutation fixation rate and past hybridization events. Reproductive parasites like Wolbachia and Cardinium might influence these processes. We discuss the role these bacteria could play in the evolutionary success of asexual species.
Assessment of age and greenness of herbarium specimens as predictors for succesful extraction and amplification of DNA
Erkens, R.H.J. ; Cross, H. ; Maas, J.W. ; Hoenselaar, K. ; Chatrou, L.W. - \ 2008
Blumea 53 (2008)2. - ISSN 0006-5196 - p. 407 - 421.
sensitive detection - mitochondrial-dna - plant specimens - ancient dna - nested-pcr - preservation - genera - degradation - annonaceae
Age and the greenness of leaves have been frequently used as indicators for selecting herbarium specimens for molecular studies. Although plant DNA extraction and amplification have been common lab procedures for the past 20 years, no studies specifically investigated the success of these indicators. Here the predictive value of age and the greenness for extraction and amplification success is assessed, using a large number of herbarium specimens from different plant groups. The investigation of these indicators is important because herbarium material is a precious commodity, and is often the only remaining floral record of now extinct ecosystems. In cases where little leaf material is available, most researchers still attempt to extract DNA. This study shows that age and greenness of leaves are unreliable indicators of extraction and amplification success, although together they can have limited usefulness. Furthermore, we found that the amount of extracted DNA from herbarium specimens decreases with c. 1% per year in age of the specimens. Therefore, researchers sometimes should refrain from using old rare specimens because chances of success are unpredictable and precious herbarium material might be wasted. The uncritical use of indicators such as age or leaf colour is therefore not recommendable. Furthermore, botanists should annotate how specimens were collected and dried because this information is essential for successful DNA extraction. Hopefully, similar studies will be reported in order to identify the best approaches to extract DNA from herbarium specimens
Population structure and historical demography of the thorny skate (Amblyraja radiata, Rajidae) in the North Atlantic
Chevolot, M. ; Wolfs, P.H.J. ; Palsson, J. ; Rijnsdorp, A.D. ; Stam, W.T. ; Olsen, J.L. - \ 2007
Marine Biology 151 (2007)4. - ISSN 0025-3162 - p. 1275 - 1286.
pleuronectes-platessa l. - ray raja-clavata - mitochondrial-dna - baltic sea - geographical-distribution - cladistic-analysis - secondary contact - genetic-structure - english-channel - fucus-serratus
Population genetic structure of the thorny skate (Amblyraja radiata) was surveyed in >300 individuals sampled from Newfoundland, Iceland, Norway, the Kattegat and the central North Sea. A 290-bp fragment of the mt cytochrome-b gene was first screened by SSCP. Sequences of SSCP haplotypes revealed 34 haplotypes, 14 of which were unique to Iceland, 3 to Newfoundland, 1 to Norway and 3 to the Kattegat. The global F ST was weak but significant. Removal of the two Kattegat locations, which were the most differentiated, resulted in no significant genetic differentiation. Haplotype diversity was high and evenly distributed across the entire Atlantic (h = 0.8) with the exception of the North Sea (h = 0.48). Statistical parsimony revealed a star-like genealogy with a central widespread haplotype. A subsequent nested clade analysis led to the inference of contiguous expansion with evidence for long distance dispersal between Newfoundland and Iceland. Historical demographic analysis showed that thorny skates have undergone exponential population expansion that started between 1.1 million and 690,000 years ago; and that the Last Glacial Maximum apparently had little effect. These results strongly differ from those of a parallel study of the thornback ray (Raja clavata) in which clear structure and former refugial areas could be identified. Although both species have similar life history traits and overlapping ranges, the continental shelf edge apparently does not present a barrier to migration in A. radiata, as it does for R. clavata
New developments in the detection and identification of processed animal proteins in feeds
Raamsdonk, L.W.D. van; Holst, C. von; Baeten, V. ; Berben, G. ; Boix, A. ; Jong, J. de - \ 2007
Animal Feed Science and Technology 133 (2007)1-2. - ISSN 0377-8401 - p. 63 - 83.
bovine spongiform encephalopathy - bone meal - monoclonal-antibody - mitochondrial-dna - mass-spectrometry - pcr detection - ruminant - spectroscopy - validation - dipeptides
It is generally accepted that the most likely route of infection of cattle with bovine spongiform encephalopathy (BSE) is by consumption of feeds containing low levels of processed animal proteins (PAPs). This likely route of infection resulted in feed bans, which were primarily aimed at ruminant feeds, and were later extended to all feeds for farmed animals. The feed bans were expected to develop into a future enforcement of the "species-to-species" ban, which prohibits only the feeding of animal-specific proteins to the same species. The species-to-species ban requires support of species-specific identification methods. In the European Union, microscopic evaluation is currently the only accepted method for the detection and characterization of PAPs in feeds, since it is possible to detect contaminations at the requested level of 1 g/kg with hardly any false negative nor positive results. This method is predominantly focused on the presence and characteristics of bone fragments, although other structures, e.g. muscle fibres, may provide circumstantial evidence of the respective animal types. Recent developments are the identification of bone fragments at the level of classes (mammal versus bird versus fish), supported by image analysis of bone characteristics. Detection of DNA and specific proteins are additional methods that can be applied for the identification of PAPs in feeds. DNA is known to be very specific for animal species and breeds, whereas proteins can also indicate the type of tissue. The latter aspect is important to differentiate between proteins that are authorised in animal nutrition from banned proteins. Improvements can be noted in recent years for both methods. For a proper application of polymerase chain reaction (PCR) to detect specific sequences of DNA, primer sets have been developed which amplify a DNA sequence shorter than approximately 100 nucleotides. Specific antibodies have been developed for protein detection of ruminant or bovine material. Recent results of various studies indicate that specific DNA and protein detection methods can detect PAPs at a contamination level of 1 g/kg. However, full validation of these methods still needs to be carried out. Other methods such as near-infrared spectroscopy (NIRS), near-infrared microscopy (NIRM), near-infrared imaging, liquid chromatography (LC) and olfactometry techniques can and will be applied for the detection of PAPs. NIRS is a non-destructive method that can be applied on-line in feed production plants. Generally, the detection limit is still too high to be applied in official control laboratories. Nevertheless, industrial application is feasible. NIRM and near-infrared imaging are techniques that allow collection of near-infrared spectra from individual particles. The level of detection is lower than 1 g/kg since it is based on the microscopic technique, in combination with the option of identification of the individual particles. LC is based on the detection and, if present, the ratio of different polypeptides. For example, carnosine is mainly present in mammals and anserine mainly found in birds. Olfactometry is based on detection of volatile non-specific agents. It is a non-destructive and fast technique. For both LC and olfactometry it appears that the presence of fish material masks the detection of proteins of land animals, even at a contamination level of 5 g/kg. Since 2003 five different proficiency studies and ring trials have been organized. The first proficiency study, allowing the participants to apply their own protocol, revealed that correct microscopic detection of 1 g/kg of mammalian PAP in the presence of 50 g fish meal/kg was realised in 0.44 of the cases. However, a bench mark study organized in the same year showed that a microscopic detection of 0.98 can be reached provided the application of an optimal protocol and a sufficient level of expertise. More recent studies showed that training, the application of a decision support system and use of an improved microscopy protocol resulted in a higher sensitivity. An attractive approach is the combination of the very low detection level of microscopy with identification by other methods. Several strategies for a combination of screening and confirmation methods are discussed in the present paper. The new developments in methodology will support current or new legislation (e.g. species-to-species ban, general application of fish meal). (c) 2006 Elsevier B.V. All rights reserved.
Badger hair in shaving brushes comes from protected Eurasian badgers
Domingo-Roura, X. ; Marmi, J. ; Ferrando, A. ; López-Giráldez, F. ; Macdonald, D.W. ; Jansman, H.A.H. - \ 2006
Biological Conservation 128 (2006)3. - ISSN 0006-3207 - p. 425 - 430.
mitochondrial-dna - cytochrome-b - identification - gene - pcr
The Eurasian badger (Meles meles) is included in Appendix III of the Bern Convention and protected by national laws in many European countries. Badger hair is used to manufacture luxury shaving brushes, although it is frequently argued that the hog badger (Arctonyx collaris), which in Europe is an introduced and unprotected species, is the origin of the hair used. We applied an extraction protocol to recover DNA from the unrooted hair of shaving brushes obtained from commercial companies in The Netherlands and Spain. The tested brushes originated from The Netherlands, Spain, France, Italy and the United Kingdom where the Eurasian badger is a protected species. We sequenced 191 bp of the mitochondrial DNA control region and 170 bp of the cytochrome b gene and compared the sequences obtained with Eurasian badger and hog badger reference sequences of the same mitochondrial DNA regions obtained in our laboratory and from GenBank. Sequences obtained from four shaving brushes were clearly hog badger sequences, whereas four sequences clustered with Eurasian badger sequences of both European and Asian origins. One of the shaving brushes made of Eurasian badger was produced in France, where it is legal to capture or trade the species under certain conditions. The remaining three brushes originated from The Netherlands, where it is illegal to possess, sell, transport or use for commercial purposes dead Eurasian badgers or products derived from them. (c) 2005 Elsevier Ltd. All rights reserved.
Genetic spatial structure of European common hamsters (Cricetus cricetus) - a result of repeated range expansion and demographic bottlenecks
Neumann, K. ; Michaux, R. ; Maak, S. ; Jansman, H.A.H. ; Kayser, A. ; Mundt, G. ; Gattermann, R. - \ 2005
Molecular Ecology 14 (2005)5. - ISSN 0962-1083 - p. 1473 - 1483.
voles microtus-agrestis - mitochondrial-dna - postglacial colonization - phylogeography - populations - microsatellites - consequences - evolution - oeconomus - sequences
The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15 00010 000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85 000147 000 bp. Expansion times fall during the last glaciation (115 00010 000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50 000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary.
Determination of processed animal proteins, including meat and bone meal, in animal feed
Gizzi, G. ; Holst, C. von; Baeten, V. ; Berben, G. ; Raamsdonk, L.W.D. van - \ 2004
Journal of AOAC International 87 (2004)6. - ISSN 1060-3271 - p. 1334 - 1341.
mitochondrial-dna - ruminant
The presence of processed animal proteins (PAP), including meat and bone meal (MBM) from various species, in animal feed was investigated. It was demonstrated that microscopy is the most reliable method for enforcing the current total MBM ban in the European Uion (EU). It was shown that near infrared microscopy (NIRM) applied to the sediment fraction of the sample is a very reliable tool for the detection of meat and bone meal in feed. The technique was suggested to be an alternative method for the detection of MBM, especially when the required instrumentation becomes more affordable.
Phylogeny of Pelargonium (Geraniaceae) based on DNA sequences from three genomes
Bakker, F.T. ; Culham, A. ; Hettiarachi, P. ; Touloumendidou, T. ; Gibby, M. - \ 2004
Taxon 53 (2004)1. - ISSN 0040-0262 - p. 17 - 31.
earliest land plants - plastid dna - mitochondrial-dna - section ligularia - chloroplast dna - sperm cells - cape flora - trnl-f - regions - pollination
Phylogenetic hypotheses for the largely South African genus Pelargonium L'Hér. (Geraniaceae) were derived based on DNA sequence data from nuclear, chloroplast and mitochondrial encoded regions. The datasets were unequally represented and comprised cpDNA trnL-F sequences for 152 taxa, nrDNA ITS sequences for 55 taxa, and mtDNA nad1 b/c exons for 51 taxa. Phylogenetic hypotheses derived from the separate three datasets were overall congruent. A single hypothesis synthesising the information in the three datasets was constructed following a total evidence approach and implementing dataset specific stepmatrices in order to correct for substitution biases. Pelargonium was found to consist of five main clades, some with contrasting evolutionary patterns with respect to biogeographic distributions, dispersal capacity, pollination biology and karyological diversification. The five main clades are structured in two (subgeneric) clades that correlate with chromosome size. One of these clades includes a "winter rainfall clade" containing more than 70% of all currently described Pelargonium species, and all restricted to the South African Cape winter rainfall region. Apart from (woody) shrubs and small herbaceous rosette subshrubs, this clade comprises a large "xerophytic" clade including geophytes, stem and leaf succulents, harbouring in total almost half of the genus. This clade is considered to be the result of in situ proliferation, possibly in response to late-Miocene and Pliocene aridification events. Nested within it is a radiation comprising c. 80 species from the geophytic Pelargonium section Hoarea, all characterised by the possession of (a series of) tunicate tubers.
Real-time PCR detection of ruminant DNA
Mendoza - Romero, L. ; Verkaar, E.L.C. ; Savelkoul, P.H. ; Catsburg, A. ; Aarts, H.J.M. ; Buntjer, J.B. ; Lenstra, J.A. - \ 2004
Journal of Food Protection 67 (2004)3. - ISSN 0362-028X - p. 550 - 554.
bovine spongiform encephalopathy - mitochondrial-dna - bone meal - species identification - animal feedstuffs - satellite dna - evolution - cattle - transmission - sequences
To control the spread of bovine spongiform encephalopathy, several DNA methods have been described for the detection of the species origin of meat and bone meal. Most of these methods are based on the amplification of a mitochondrial DNA segment. We have developed a semiquantitative method based on real-time PCR for detection of ruminant DNA, targeting an 88-bp segment of the ruminant short interspersed nuclear element Bov-A2. This method is specific for ruminants and is able to detect as little as 10 fg of bovine DNA. Autoclaving decreased the amount of detectable DNA, but positive signals were observed in feeding stuff containing 10␋ovine material if this had not been rendered in accordance with the regulations, i.e., heated at 134°C for 3 instead of 20 min.
The evolution of non-reciprocal nuclear exchange in mushrooms as a consequence of genomic conflict
Aanen, D.K. ; Kuyper, T.W. ; Debets, A.J.M. ; Hoekstra, R.F. - \ 2004
Proceedings of the Royal Society. B: Biological Sciences 271 (2004)1545. - ISSN 0962-8452 - p. 1235 - 1241.
basidiomycete coprinus-cinereus - mitochondrial-dna - uniparental inheritance - pleurotus-ostreatus - podospora-anserina - pheromone - specificities - homokaryons - speciation - mechanisms
Heterothallic mushrooms accomplish sex by exchanging nuclei without cytoplasm. Hyphal fusions occur between haploid mycelia resulting from germinated spores and subsequent reciprocal nuclear exchange without cytoplasmic mixing. The resulting dikaryon is therefore a cytoplasmic mosaic with uniformly distributed nuclei (two in each cell). Cytoplasmic inheritance is doubly uniparental: both mated monokaryons can potentially transmit their cytoplasm to the sexual spores, but normally only a single type per spore is found. Intracellular competition between mitochondria is thus limited, but at the dikaryon level, the two types of mitochondria compete over transmission. This creates the conditions for genomic conflict: within the dikaryon, a selfish mitochondrial mutant with increased relative transmission can be favoured, but selection between dikaryons will act against such a mitochondrial mutant. Moreover, because nuclear fitness is directly dependent on dikaryon fitness, a reduction in dikaryon fitness directly conflicts with nuclear interests. We propose that genomic conflict explains the frequent occurrence of non-reciprocal nuclear exchange in mushrooms. With non-reciprocal exchange, one monokaryon donates a nucleus and the other accepts it, but not vice versa as in the typical life cycle. We propose a model where non-reciprocal nuclear exchange is primarily driven by mitochondria inducing male sterility and the evolution of nuclear suppressors
Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster
Sabater-Munoz, B. ; Ham, R.C.H.J. van; Moya, A. ; Silva, F.J. ; Latorre, A. - \ 2004
Journal of Bacteriology 186 (2004)9. - ISSN 0021-9193 - p. 2646 - 2654.
anthranilate synthase trpeg - endosymbiotic bacteria - genome sequence - molecular characterization - symbiotic bacteria - schizaphis-graminum - mitochondrial-dna - escherichia-coli - aphids - plasmid
In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes (leuA, -B, -C, and -D) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the variability in the position of the leucine cluster in the chromosome may be interpreted as resulting from independent insertions from an ancestral plasmid-borne leucine gene. These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome
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