TY - JOUR A1 - Averbeck, Christiane A1 - Apio, Ann A1 - Plath, Martin A1 - Wronski, Torsten T1 - Environmental parameters and anthropogenic effects predicting the spatial distribution of wild ungulates in the Akagera savannah ecosystem N2 - Savannah areas affected by human activities such as livestock keeping and agriculture are often characterized by shifts in landscape structuring, with a predominance of few(er) habitat types. This is typically accompanied by pronounced changes in the communities of ungulates. The aim of this study was to find out whether shifts in ungulate communities in Lake Mburo National Park (LMNP) are primarily predicted by an alteration in the composition of the preferred habitat types or if more complex interactions between habitat changes and the prevalence of ungulates occur. Monthly road counts were used to establish the number of eleven ungulate species in LMNP and adjacent unprotected Ankole Ranching Scheme. The common duiker (Sylvicapra grimmia campbelliae Gray, 1843) was found in more abundance in disturbed areas, while showing a significant change in habitat use. Common duiker tended to use the vegetation type otherwise used by the bushbuck (Tragelaphus scriptus dama Neumann, 1902). Our results support the claim that the occurrence of ungulates is not only directly affected by the availability of 'suitable' habitats, but behavioural plasticity and competitive exclusion also need to be considered. Y1 - 2009 UR - http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2028 U6 - https://doi.org/10.1111/j.1365-2028.2009.01076.x SN - 0141-6707 ER - TY - JOUR A1 - Averbeck, Christiane A1 - Apio, Ann A1 - Plath, Martin A1 - Wronski, Torsten T1 - Hunting differentially affects mixed-sex and bachelor-herds in a gregarious ungulate, the impala (Aepyceros melampus: Bovidae) N2 - We investigated herd-sizes and herd-compositions of Impala (Aepyceros melampus) inside a protected area [Lake Mburo National Park (LMNP) in western Uganda] and the unprotected adjacent ranchland [the Ankole Ranching Scheme (ARS)]. Impala experience intense hunting and poaching in the study area, and poaching is especially strong on the ARS. We found evidence for changes in overall group-sizes in both mixed-sex and pure bachelor herds between areas in and outside LMNP. Mixed-sex herds strongly decreased in size outside the National Park, but bachelor herds even slightly increased in size. While the group-composition of mixed-sex herds was very similar in areas in and outside LMNP, bachelor herds comprised more yearlings and subadult males on the ARS. Our study suggests that effects of hunting and other human nuisance may differ between herd types: mixed herds probably decrease in size because females are more strongly hunted. Around LMNP, impala are usually hunted using nets and spears, thereby increasing the hunters' chance of being injured. Poachers therefore prefer hornless females (and their calves), as it is less dangerous to handle net-caught females than males. As a result, males are less hunted, but increased vigilance and, therefore, reduced aggression among the members of a bachelor herd, may account for the observed increase in herd sizes and changes in group-compositions. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0141-6707 U6 - https://doi.org/10.1111/j.1365-2028.2009.01118.x SN - 0141-6707 ER - TY - JOUR A1 - Avcilar-Kucukgoze, Irem A1 - Bartholomäus, Alexander A1 - Varela, Juan A. Cordero A1 - Kaml, Robert Franz-Xaver A1 - Neubauer, Peter A1 - Budisa, Nediljko A1 - Ignatova, Zoya T1 - Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli JF - Nucleic acids research N2 - Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth. Y1 - 2016 U6 - https://doi.org/10.1093/nar/gkw697 SN - 0305-1048 SN - 1362-4962 VL - 44 SP - 8324 EP - 8334 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Avcilar-Kucukgoze, Irem T1 - Effect of tRNA Aminoacylation and Cellular Resources Allocation on the Dynamics of Translation in Escherichia coli Y1 - 2016 ER - TY - JOUR A1 - Autenrieth, Marijke A1 - Hartmann, Stefanie A1 - Lah, Ljerka A1 - Roos, Anna A1 - Dennis, Alice B. A1 - Tiedemann, Ralph T1 - High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) JF - Molecular ecology resources N2 - The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation. KW - cetaceans KW - genomics/proteomics KW - mammals KW - molecular evolution Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12932 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1469 EP - 1481 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Autenrieth, Marijke A1 - Ernst, Anja A1 - Deaville, Rob A1 - Demaret, Fabien A1 - Ijsseldijk, Lonneke L. A1 - Siebert, Ursula A1 - Tiedemann, Ralph T1 - Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea T2 - Mammalian biology = Zeitschrift für Säugetierkunde N2 - The globally distributed sperm whale (Physeter macrocephalus) has a partly matrilineal social structure with predominant male dispersal. At the beginning of 2016, a total of 30 male sperm whales stranded in five different countries bordering the southern North Sea. It has been postulated that these individuals were on a migration route from the north to warmer temperate and tropical waters where females live in social groups. By including samples from four countries (n = 27), this event provided a unique chance to genetically investigate the maternal relatedness and the putative origin of these temporally and spatially co-occuring male sperm whales. To utilize existing genetic resources, we sequenced 422 bp of the mitochondrial control region, a molecular marker for which sperm whale data are readily available from the entire distribution range. Based on four single nucleotide polymorphisms (SNPs) within the mitochondrial control region, five matrilines could be distinguished within the stranded specimens, four of which matched published haplotypes previously described in the Atlantic. Among these male sperm whales, multiple matrilineal lineages co-occur. We analyzed the population differentiation and could show that the genetic diversity of these male sperm whales is comparable to the genetic diversity in sperm whales from the entire Atlantic Ocean. We confirm that within this stranding event, males do not comprise maternally related individuals and apparently include assemblages of individuals from different geographic regions. (c) 2017 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved. KW - Mitochondrial DNA KW - Maternal relationships KW - Population genetics KW - Migration KW - Marine mammals Y1 - 2018 U6 - https://doi.org/10.1016/j.mambio.2017.09.003 SN - 1616-5047 SN - 1618-1476 VL - 88 SP - 156 EP - 160 PB - Elsevier CY - München ER - TY - THES A1 - Autenrieth, Marijke T1 - Population genomics of two odontocetes in the North Atlantic and adjacent waters BT - Evolutionary history and conservation implications N2 - Due to continuously intensifying human usage of the marine environment worldwide ranging cetaceans face an increasing number of threats. Besides whaling, overfishing and by-catch, new technical developments increase the water and noise pollution, which can negatively affect marine species. Cetaceans are especially prone to these influences, being at the top of the food chain and therefore accumulating toxins and contaminants. Furthermore, they are extremely noise sensitive due to their highly developed hearing sense and echolocation ability. As a result, several cetacean species were brought to extinction during the last century or are now classified as critically endangered. This work focuses on two odontocetes. It applies and compares different molecular methods for inference of population status and adaptation, with implications for conservation. The worldwide distributed sperm whale (Physeter macrocephalus) shows a matrilineal population structure with predominant male dispersal. A recently stranded group of male sperm whales provided a unique opportunity to investigate male grouping for the first time. Based on the mitochondrial control region, I was able to infer that male bachelor groups comprise multiple matrilines, hence derive from different social groups, and that they represent the genetic variability of the entire North Atlantic. The harbor porpoise (Phocoena phocoena) occurs only in the northern hemisphere. By being small and occurring mostly in coastal habitats it is especially prone to human disturbance. Since some subspecies and subpopulations are critically endangered, it is important to generate and provide genetic markers with high resolution to facilitate population assignment and subsequent protection measurements. Here, I provide the first harbour porpoise whole genome, in high quality and including a draft annotation. Using it for mapping ddRAD seq data, I identify genome wide SNPs and, together with a fragment of the mitochondrial control region, inferred the population structure of its North Atlantic distribution range. The Belt Sea harbors a distinct subpopulation oppose to the North Atlantic, with a transition zone in the Kattegat. Within the North Atlantic I could detect subtle genetic differentiation between western (Canada-Iceland) and eastern (North Sea) regions, with support for a German North Sea breading ground around the Isle of Sylt. Further, I was able to detect six outlier loci which show isolation by distance across the investigated sampling areas. In employing different markers, I could show that single maker systems as well as genome wide data can unravel new information about population affinities of odontocetes. Genome wide data can facilitate investigation of adaptations and evolutionary history of the species and its populations. Moreover, they facilitate population genetic investigations, providing a high resolution, and hence allowing for detection of subtle population structuring especially important for highly mobile cetaceans. N2 - Mit der immer stärker zunehmenden Nutzung des marinen Lebensraumes durch den Menschen, häufen sich auch die Bedrohungen, wie beispielsweise Lebensraumzerstörungen, denen Cetacea ausgesetzt sind. Die Folgen aus Walfang, Überfischung und Beifang, wie auch die stärkere Verschmutzung der Meere sowie die Zunahme des generellen Lärmpegels, haben negative Effekte auf eine Vielzahl mariner Arten. Cetacea sind besonders anfällig für diese Störungen, da sie einerseits am Ende der Nahrungskette stehen und somit besonders Schadstoffe, wie bspw. PBEs, in ihren Körpern akkumulieren und andererseits durch ihr hoch angepasstes Gehör äußerst sensibel gegenüber Geräuschstörungen sind. Im Laufe des letzten Jahrhunderts wurden einige marine Säugetiere bereits ausgerottet oder fast bis an den Rand des Aussterbens gebracht. Diese Arbeit konzentriert sich auf zwei Zahnwalarten, die in ihrer Biologie und Populationsstruktur sehr verschieden sind. Sie bieten die Möglichkeit, verschiedene Methoden der Naturschutz- und Populationsgenetik anzuwenden und zu vergleichen. Der weltweit verbreitete Pottwal ist matrilineal organisiert mit Weibchen, die in sozialen Gruppen in der Nähe des Äquators leben, und Männchen, die in kleinen Gruppen zu den Polen migrieren. Zum Jahresbeginn 2016 strandete eine Gruppe junger männlicher Pottwale entlang der Nordsee. Dieses Ereignis bot die einzigartige Chance, erstmals die genetische Zusammensetzung einer männlichen Pottwalgruppe zu untersuchen. Basierend auf der mitochondrialen Kontrollregion, konnte ich zeigen, dass sie von mehreren Matrilinien abstammen und in ihrer Gesamtheit die genetische Vielfalt der nordatlantischen Gesamtpopulation repräsentieren. Der Schweinswal ist innerhalb der nördlichen Hemisphäre weit verbreitet. Durch seine kleine Körpergrösse und die Präferenz für küstennahe Habitate ist er besonders anfällig gegenüber negativen anthropogenen Einflüssen. Da sowohl eine seiner Unterarten als auch einige Subpopulationen durch die IUCN als stark bedroht klassifiziert sind, ist es besonders wichtig die genetische Struktur dieser Art und ihrer Populationen zu erfassen und hochauflösende Markersysteme zu generieren, um verlässliche Informationen zum Status lokaler Populationen für weiterführende Naturschutzmaßnahmen bereitzustellen. In dieser Arbeit konnte ich die erste komplette Genomsequenz des Schweinwal in hoher Qualität bereitstellen und sie für die Analyse von ddRAD-Daten als Referenz nutzen. Mittles genomweit verteilter SNPs, sowie einem Abschnitt der mitochondrialen Kontrollregion zeigte sich, dass die Schweinswale in der Beltsee eine eigenständige Population bilden, mit einer Transitionszone zum Nord-Atlantik im Kattegat. Innerhalb des Nord-Atlantiks zeigten sich Unterschiede zwischen West (Kanada-Island) und Ost (Nordsee), sowie eine Abgrenzung deutscher Schweinswale um die Insel Sylt. Außerdem konnte ich sechs SNPs identifizieren, welche die populationsgenetische Auflösung im Nordatlantik und geographischen Distanz wiederspiegeln. Durch den Vergleich verschiedener Markersysteme konnte ich zeigen, dass sowohl einzelne Marker als auch genomweite Marker neue Erkenntnisse zu Populationsstrukturen und Anpassungen von Zahnwalen liefern. Durch die hohe Mobilität und den schwer zugänglichen Lebensraum mariner Säugetiere sind hochauflösende genetische Markersysteme der Schlüssel für ein besseres Verständnis und den Schutz dieser Arten. KW - genomics KW - population genetics KW - conservation KW - evolution KW - whole genome KW - toothed whales KW - Genomik KW - Populationsgenetik KW - Naturschutz KW - Evolution KW - Zahnwale Y1 - 2020 ER - TY - JOUR A1 - Augusiak, Jacqueline A1 - Van den Brink, Paul J. A1 - Grimm, Volker T1 - Merging validation and evaluation of ecological models to 'evaludation': A review of terminology and a practical approach JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Confusion about model validation is one of the main challenges in using ecological models for decision support, such as the regulation of pesticides. Decision makers need to know whether a model is a sufficiently good representation of its real counterpart and what criteria can be used to answer this question. Unclear terminology is one of the main obstacles to a good understanding of what model validation is, how it works, and what it can deliver. Therefore, we performed a literature review and derived a standard set of terms. 'Validation' was identified as a catch-all term, which is thus useless for any practical purpose. We introduce the term 'evaludation', a fusion of 'evaluation' and 'validation', to describe the entire process of assessing a model's quality and reliability. Considering the iterative nature of model development, the modelling cycle, we identified six essential elements of evaludation: (i) 'data evaluation' for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) 'conceptual model evaluation' for examining the simplifying assumptions underlying a model's design; (iii) 'implementation verification' for testing the model's implementation in equations and as a computer programme; (iv) 'model output verification' for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) 'model analysis' for exploring the model's sensitivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) 'model output corroboration' for comparing model output to new data and patterns that were not used for model development and parameterisation. Currently, most decision makers require 'validating' a model by testing its predictions with new experiments or data. Despite being desirable, this is neither sufficient nor necessary for a model to be useful for decision support. We believe that the proposed set of terms and its relation to the modelling cycle can help to make quality assessments and reality checks of ecological models more comprehensive and transparent. (C) 2013 Elsevier B.V. All rights reserved. KW - Model validation KW - Terminology KW - Decision support KW - Documentation KW - Ecological models KW - Risk assessment Y1 - 2014 U6 - https://doi.org/10.1016/j.ecolmodel.2013.11.009 SN - 0304-3800 SN - 1872-7026 VL - 280 SP - 117 EP - 128 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Audisio, Paolo A1 - Cline, Andrew R. A1 - Solano, Emanuela A1 - Mancini, Emiliano A1 - Lamanna, Francesco A1 - Antonini, Gloria A1 - Trizzino, Marco T1 - A peculiar new genus and species of pollen-beetle (Coleoptera, Nitidulidae) from eastern Africa, with a molecular phylogeny of related Meligethinae JF - Systematics and biodiversity KW - new species KW - new genus KW - molecular analysis KW - pollen-beetles KW - host-plants KW - Asteraceae KW - Kenya KW - Tarchonanthopria freidbergi Y1 - 2014 U6 - https://doi.org/10.1080/14772000.2013.877539 SN - 1477-2000 SN - 1478-0933 VL - 12 IS - 1 SP - 77 EP - 91 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Attermeyer, Katrin A1 - Tittel, Joerg A1 - Allgaier, Martin A1 - Frindte, Katharina A1 - Wurzbacher, Christian A1 - Hilt, Sabine A1 - Kamjunke, Norbert A1 - Grossart, Hans-Peter T1 - Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition JF - Microbial ecology N2 - The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties. KW - Bacterial growth efficiency KW - Continuous cultures KW - Carbon decomposition KW - Leaf litter KW - Photolysis Y1 - 2015 U6 - https://doi.org/10.1007/s00248-014-0549-4 SN - 0095-3628 SN - 1432-184X VL - 69 IS - 2 SP - 361 EP - 371 PB - Springer CY - New York ER -