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Seyahooei M.A.,Leiden University | van Alphen J.J.M.,Institute for Biodiversity and Ecosystem Dynamics | Kraaijeveld K.,Leiden University
BMC Ecology | Year: 2011

Background: The genetic structure of populations can be influenced by geographic isolation (including physical distance) and ecology. We examined these effects in Leptopilina boulardi, a parasitoid of Drosophila of African origin and widely distributed over temperate and (sub) tropical climates.Results: We sampled 11 populations of L. boulardi from five climatic zones in Iran and measured genetic differentiation at nuclear (Amplified Fragment Length Polymorphism; AFLP) and mitochondrial (Cytochrome Oxidase I; COI) loci. An Analysis of Molecular Variance (AMOVA) for the AFLP data revealed that 67.45% of variation resided between populations. No significant variation was observed between climatic zones. However, a significant difference was detected between populations from the central (dry) regions and those from the wetter north, which are separated by desert. A similarly clear cut genetic differentiation between populations from the central part of Iran and those from the north was observed by UPGMA cluster analysis and Principal Coordinates Analysis (PCO). Both UPGMA and PCO further separated two populations from the very humid western Caspian Sea coast (zone 3) from other northern populations from the temperate Caspian Sea coastal plain (zone 2), which are connected by forest. One population (Nour) was genetically intermediate between these two zones, indicating some gene flow between these two groups of populations. In all analyses a mountain population, Sorkhabad was found to be genetically identical to those from the nearby coastal plain (zone 2), which indicates high gene flow between these populations over a short geographical distance. One population from the Caspian coast (Astaneh) was genetically highly diverged from all other populations. A partial Mantel test showed a highly significant positive correlation between genetic and geographic distances, as well as separation by the deserts of central Iran. The COI sequences were highly conserved among all populations.Conclusion: The Iranian populations of L. boulardi showed clear genetic structure in AFLP profiles, but not in COI sequence data. The transfer of fruits containing Drosophila larvae parasitized by L. boulardi appears to have caused some unexpected gene flow and changed the genetic composition of populations, particularly in urban areas. Nevertheless, our results suggest that climate, geographic distance and physical barriers may all have contributed to the formation of genetically distinct populations of L. boulardi. Inevitably, there will be overlap between the portions of variance explained by these variables. Disentangling the relative contributions of climate and geography to the genetic structure of this species will require additional sampling. © 2011 Seyahooei et al; licensee BioMed Central Ltd.


Gerla D.J.,Netherlands Institute of Ecology | Mooij W.M.,Netherlands Institute of Ecology | Huisman J.,Institute for Biodiversity and Ecosystem Dynamics
Oikos | Year: 2011

Photoinhibition is characterised by a decreasing rate of photosynthesis with increasing light. It occurs in many photosynthetic organisms and is especially apparent in phytoplankton species sensitive to high light. Yet, the population and community level consequences of photoinhibition are not well understood. Here, we present a resource competition model that includes photoinhibition. The model shows that, in strong light, photoinhibition leads to an increase of the specific growth rate with increasing population density due to self-shading. This so-called Allee effect can be either weak or strong. In monoculture, a strong Allee effect results in two alternative stable states. A low population density does not provide sufficient shade to protect itself against photoinhibition, such that the population goes extinct. Conversely, above a threshold population density the population may create sufficiently turbid conditions to suppress photoinhibition, so that the population can establish itself. When several species compete for light, a species which cannot establish itself due to photoinhibition can be facilitated by other species less sensitive to photoinhibition. If such facilitators are absent, photoinhibition may cause alternative stable states in community composition. Since each alternative stable state is dominated by a single species, photoinhibition does not favour species coexistence. The model predictions are consistent with published competition experiments, and illustrate the complex effects of photoinhibition on community assembly. © 2011 The Authors. Oikos © 2011 Nordic Society Oikos.


van Maanen R.,Institute for Biodiversity and Ecosystem Dynamics | Vila E.,Agrobio S.L. | Sabelis M.W.,Institute for Biodiversity and Ecosystem Dynamics | Janssen A.,Institute for Biodiversity and Ecosystem Dynamics
Experimental and Applied Acarology | Year: 2010

The broad mite is a serious pest of a variety of crops worldwide. Several phytoseiid mites have been described to control these mites. However, broad mites are still one of the major pest problems on greenhouse pepper in South-eastern Spain. The generalist predatory mite A. swirskii is widely used against other pests of pepper plants such as thrips and whiteflies, the latter being a vector of broad mites. We assessed the potential of A. swirskii to control broad mites. The oviposition rate of A. swirskii on a diet of broad mites was lower than on a diet of pollen, but higher than oviposition in the absence of food. Population-dynamical experiments with A. swirskii on single sweet pepper plants in a greenhouse compartment showed successful control of broad mites. © 2010 The Author(s).


van Geel B.,Institute for Biodiversity and Ecosystem Dynamics | Heijnis H.,Australian Nuclear Science and Technology Organisation | Charman D.J.,University of Exeter | Thompson G.,University of Exeter | Engels S.,Institute for Biodiversity and Ecosystem Dynamics
Holocene | Year: 2014

The nature and cause of the so-called 2.8 kyr BP event have been a subject of much debate. Peat sequences have provided much of the evidence for this event, but the process link between climate and peatland response is not well understood. Multiproxy, high-resolution analysis of a core from Bargerveen in the eastern Netherlands based on pollen, non-pollen palynomorphs, testate amoebae and geochemistry identified an abrupt shift from relatively dry to extremely wet conditions. Radiocarbon-based wiggle-match dating (WMD) and biostratigraphy based on the pollen record show that this shift in local hydrology occurred around 2800 cal. yr BP. We interpret an erosional hiatus lasting up to 950 years immediately prior to this, as the effect of a bog burst after excessive rainfall. This phenomenon was not limited to our sampling location but occurred over a large part of the former Bargerveen. Peat at the hiatus contains microfossils that reflect temporary eutrophication as a consequence of local fires and secondary decomposition because of increased drainage after the erosion event. Our data show how detailed multiproxy analyses can elucidate the past response of peatlands to changing climate and suggest that the climatic change in northwest Europe at this time caused major non-linear disruption to these ecosystems. © The Author(s) 2014.


News Article | April 13, 2016
Site: phys.org

How diet has affected the evolution of the 10,000 bird species in the world is still a mystery to evolutionary biology. A study by Daniel Kissling of the Institute for Biodiversity and Ecosystem Dynamics (UvA) and colleagues from the University of São Paulo and the University of Utah shows how diet preferences have influenced bird diversification over millions of years. The findings were published in Nature Communications. Since the seminal work by Charles Darwin, it is know that dietary habits of birds can affect the evolution of species, such as the beak sizes of Galapagos finches. However, birds show an astonishing diversity of species and dietary adaptations, ranging from very small nectar-feeding hummingbirds to large carnivorous eagles. How such diverse dietary preferences ultimately lead to differences in diversification dynamics (i.e. the balance between speciation and extinction) of different birds has not yet been examined. The researchers compiled an impressive diet dataset of almost all bird species in the world together with a large phylogenetic tree that represent the relatedness of all bird species. Using models of trait-dependent diversification, they then showed that omnivorous bird lineages (with species that feed on many different food items) have lower rates of speciation (i.e. generating less new species) and higher rates of extinction (i.e. losing more existing species) than species which prefer specific food items such as fruits, nectar, or insects. Furthermore, the researchers also found that over deep evolutionary time birds which are specialized on a particular food item often add other food items to their diets, resulting in evolving transitions into omnivory. 'I was really surprised to find that omnivores preferentially originate via transitions, and not through speciation', says lead author and PhD student Gustavo Burin from the University of São Paulo. Together with the low speciation rates and high extinction rates, these high transition rates indicate that omnivores originate from more specialized birds that expand their diets, rather than directly through speciation of omnivorous bird clades. 'We suggest that this is caused by resource competition, climate instability, and deep-time availability of food resources', says Burin. High transition rates towards omnivory may arise in times when food is harder to find or when it is temporally unavailable. Expanding these findings to the current human-driven changes on our planet the researchers expect that shifts in competitive dynamics between generalists and specialists will occur. 'Human activities such as habitat destruction and other global change drivers eliminate the resources of many specialist species', says Daniel Kissling from University of Amsterdam. This means that specialists are currently at higher risk of extinction than generalists. 'This will dramatically change the ecology and evolution of life on Earth because generalists are now favoured at the expense of specialists', explains Kissling. Ultimately, this will affect the functioning of ecosystems and the services that nature provides to humanity. Explore further: Darwin 2.0: Scientists shed new light on how species diverge More information: Gustavo Burin et al. Omnivory in birds is a macroevolutionary sink, Nature Communications (2016). DOI: 10.1038/ncomms11250


Falara V.,University of Michigan | Alba J.M.,Institute for Biodiversity and Ecosystem Dynamics | Kant M.R.,Institute for Biodiversity and Ecosystem Dynamics | Schuurink R.C.,University of Amsterdam | Pichersky E.,University of Michigan
Plant Physiology | Year: 2014

Many angiosperm plants, including basal dicots, eudicots, and monocots, emit (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene, which is derived from geranyllinalool, in response to biotic challenge. An Arabidopsis (Arabidopsis thaliana) geranyllinalool synthase (GLS) belonging to the e/f clade of the terpene synthase (TPS) family and two Fabaceae GLSs that belong to the TPS-g clade have been reported, making it unclear which is the main route to geranyllinalool in plants. We characterized a tomato (Solanum lycopersicum) TPS-e/f gene, TPS46, encoding GLS (SlGLS) and its homolog (NaGLS) from Nicotiana attenuata.The Kmvalue of SlGLS for geranylgeranyl diphosphate was 18.7 μM, with a turnover rate value of 6.85 s-1.In leaves and flowers of N. attenuata, which constitutively synthesize 17-hydroxygeranyllinalool glycosides, NaGLS is expressed constitutively, but the gene can be induced in leaves with methyl jasmonate. In tomato, SlGLS is not expressed in any tissue under normal growth but is induced in leaves by alamethicin and methyl jasmonate treatments. SlGLS, NaGLS, AtGLSs, and several other GLSs characterized only in vitro come from four different eudicot families and constitute a separate branch of the TPS-e/f clade that diverged from kaurene synthases, also in the TPS-e/f clade, before the gymnosperm-angiosperm split. The early divergence of this branch and the GLS activity of genes in this branch in diverse eudicot families suggest that GLS activity encoded by these genes predates the angiosperm-gymnosperm split. However, although a TPS sequence belonging to this GLS lineage was recently reported from a basal dicot, no representative sequences have yet been found in monocot or nonangiospermous plants. © 2014 American Society of Plant Biologists. All Rights Reserved.


Benschop C.C.G.,Netherlands Forensic Institute | Wiebosch D.C.,Netherlands Forensic Institute | Kloosterman A.D.,Netherlands Forensic Institute | Kloosterman A.D.,Institute for Biodiversity and Ecosystem Dynamics | Sijen T.,Netherlands Forensic Institute
Forensic Science International: Genetics | Year: 2010

In the examination of sexual assault cases, DNA typing of vaginal samples mostly occurs after differential DNA extraction. Notwithstanding the differential extraction method, the DNA profiles from the seminal fraction often show the male alleles at low-level in combination with female alleles. This unfavorable ratio male to female DNA is due to a limited amount of sperm cells and an overwhelming quantity of female cells. In this study, we compared standard cotton and nylon flocked swabs for post-coital vaginal sampling. Twelve couples donated 88 vaginal swabs - 44 cotton, 44 nylon flocked - which were taken with a time since intercourse (TSI) up to 84 h. These vaginal swabs were sorted into categories on the basis of the TSI and submitted to (1) microscopic examination for the presence of male cells, (2) presumptive tests for the detection of seminal fluid and (3) DNA typing. Cellular elution was found to be 6-fold more efficient from the nylon flocked swabs. This makes microscopic analysis less time consuming as the higher cell yield and better cell morphology simplify detection of male cells. Both swab types reveal similar results regarding presumptive tests and male DNA typing. Positive presumptive tests (RSID-semen and PSA) were obtained up to 60 h TSI and male autosomal profiles up to 72 h TSI. Interestingly, over 50% of the samples negative for both presumptive tests resulted in informative male STR profiles. After differential extraction, less DNA was left on the nylon flocked swabs and more male DNA was isolated. Our results imply that the use of nylon flocked swabs for vaginal sampling will improve microscopic analysis and DNA typing in the medical forensic investigation of sexual assault cases. © 2009 Elsevier Ireland Ltd. All rights reserved.


Hammer J.,Institute for Biodiversity and Ecosystem Dynamics | Kraak M.H.S.,Institute for Biodiversity and Ecosystem Dynamics | Parsons J.R.,Institute for Biodiversity and Ecosystem Dynamics
Reviews of Environmental Contamination and Toxicology | Year: 2012

Plastics are one of the most widely used materials in the world; they are broadly integrated into today's lifestyle and make a major contribution to almost all product areas. The typical characteristics that render them so useful relate primarily to the fact that they are both flexible and durable. These characteristics are very useful when plastics are used in everyday life. But when plastics are discarded into the environment they can persist for very long periods of time. Because of their nearly indestructible morphology and the toxins they contain, plastics can seriously affect ecosystems (UNEP 2005). © 2012 Springer Science+Business Media, LLC.


Glas J.J.,Institute for Biodiversity and Ecosystem Dynamics | Schimmel B.C.J.,Institute for Biodiversity and Ecosystem Dynamics | Alba J.M.,Institute for Biodiversity and Ecosystem Dynamics | Escobar-Bravo R.,Subtropical and Mediterranean Horticulture Institute La Mayora IHSM | And 2 more authors.
International Journal of Molecular Sciences | Year: 2012

Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant's secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products that can be used by the pharmaceutical industry, although many of these substances have evolved to provide the plant with protection against herbivores and pathogens. The storage compartment of glandular trichomes usually is located on the tip of the hair and is part of the glandular cell, or cells, which are metabolically active. Trichomes and their exudates can be harvested relatively easily, and this has permitted a detailed study of their metabolites, as well as the genes and proteins responsible for them. This knowledge now assists classical breeding programs, as well as targeted genetic engineering, aimed to optimize trichome density and physiology to facilitate customization of essential oil production or to tune biocide activity to enhance crop protection. We will provide an overview of the metabolic diversity found within plant glandular trichomes, with the emphasis on those of the Solanaceae, and of the tools available to manipulate their activities for enhancing the plant's resistance to pests. © 2012 by the authors; licensee MDPI, Basel, Switzerland.


van Geel B.,University of Amsterdam | Guthrie R.D.,University of Alaska Fairbanks | Altmann J.G.,Institute for Biodiversity and Ecosystem Dynamics | Broekens P.,University of Amsterdam | And 6 more authors.
Quaternary Science Reviews | Year: 2011

Dung from a mammoth was preserved under frozen conditions in Alaska. The mammoth lived during the early part of the Late Glacial interstadial (ca 12,300 BP). Microfossils, macroremains and ancient DNA from the dung were studied and the chemical composition was determined to reconstruct both the paleoenvironment and paleobiology of this mammoth. Pollen spectra are dominated by Poaceae, Artemisia and other light-demanding taxa, indicating an open, treeless landscape ('mammoth steppe'). Fruits and seeds support this conclusion. The dung consists mainly of cyperaceous stems and leaves, with a minor component of vegetative remains of Poaceae. Analyses of fragments of the plastid rbcL gene and trnL intron and nrITS1 region, amplified from DNA extracted from the dung, supplemented the microscopic identifications. Many fruit bodies with ascospores of the coprophilous fungus Podospora conica were found inside the dung ball, indicating that the mammoth had eaten dung. The absence of bile acids points to mammoth dung. This is the second time that evidence for coprophagy of mammoths has been derived from the presence of fruit bodies of coprophilous fungi in frozen dung. Coprophagy might well have been a common habit of mammoths. Therefore, we strongly recommend that particular attention should be given to fungal remains in future fossil dung studies. © 2010 Elsevier Ltd.

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