TY - GEN A1 - Lenzner, Bernd A1 - Magallon, Susana A1 - Dawson, Wayne A1 - Kreft, Holger A1 - König, Christian A1 - Pergl, Jan A1 - Pysek, Petr A1 - Weigelt, Patrick A1 - van Kleunen, Mark A1 - Winter, Marten A1 - Dullinger, Stefan A1 - Essl, Franz T1 - Role of diversification rates and evolutionary history as a driver of plant naturalization success T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Human introductions of species beyond their natural ranges and their subsequent establishment are defining features of global environmental change. However, naturalized plants are not uniformly distributed across phylogenetic lineages, with some families contributing disproportionately more to the global alien species pool than others. Additionally, lineages differ in diversification rates, and high diversification rates have been associated with characteristics that increase species naturalization success. Here, we investigate the role of diversification rates in explaining the naturalization success of angiosperm plant families. We use five global data sets that include native and alien plant species distribution, horticultural use of plants, and a time-calibrated angiosperm phylogeny. Using phylogenetic generalized linear mixed models, we analysed the effect of diversification rate, different geographical range measures, and horticultural use on the naturalization success of plant families. We show that a family's naturalization success is positively associated with its evolutionary history, native range size, and economic use. Investigating interactive effects of these predictors shows that native range size and geographic distribution additionally affect naturalization success. High diversification rates and large ranges increase naturalization success, especially of temperate families. We suggest this may result from lower ecological specialization in temperate families with large ranges, compared with tropical families with smaller ranges. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1363 KW - alien species KW - evolution KW - geographic distribution KW - invasion success KW - plant naturalization KW - range size Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569996 SN - 1866-8372 IS - 5 ER - TY - GEN A1 - Ehrlich, Elias A1 - Kath, Nadja Jeanette A1 - Gaedke, Ursula T1 - The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1390 KW - functional traits KW - community ecology KW - evolution KW - lake KW - mechanisms KW - diversity KW - plankton KW - fitness KW - maintenance KW - coexistence Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-513956 SN - 1866-8372 IS - 6 ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR BT - an R package for individual-based simulation of spatial changes JF - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - https://doi.org/10.1111/ecog.05689 SN - 1600-0587 VL - 44 IS - 10 SP - 1443 EP - 1452 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Qiu, Liang A1 - Zhang, Haoran A1 - Bick, Thomas A1 - Martin, Johannes A1 - Wendler, Petra A1 - Böker, Alexander A1 - Glebe, Ulrich A1 - Xing, Chengfen T1 - Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition N2 - Glyco-assemblies derived from amphiphilic sugar-decorated block copolymers (ASBCs) have emerged prominently due to their wide application, for example, in biomedicine and as drug carriers. However, to efficiently construct these glyco-assemblies is still a challenge. Herein, we report an efficient technology for the synthesis of glyco-inside nano-assemblies by utilizing RAFT polymerization of a galactose-decorated methacrylate for polymerization-induced self-assembly (PISA). Using this approach, a series of highly ordered glyco-inside nano-assemblies containing intermediate morphologies were fabricated by adjusting the length of the hydrophobic glycoblock and the polymerization solids content. A specific morphology of complex vesicles was captured during the PISA process and the formation mechanism is explained by the morphology of its precursor and intermediate. Thus, this method establishes a powerful route to fabricate glyco-assemblies with tunable morphologies and variable sizes, which is significant to enable the large-scale fabrication and wide application of glyco-assemblies. KW - galactose-decorated monomer KW - glyco-inside nano-assemblies KW - morphology KW - evolution KW - PISA KW - RAFT dispersion polymerization Y1 - 2021 U6 - https://doi.org/10.1002/anie.202015692 SN - 1433-7851 SN - 1521-3773 VL - 60 IS - 20 SP - 11098 EP - 11103 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Hermanussen, Michael A1 - Erofeev, Sergei A1 - Scheffler, Christiane T1 - The socio-endocrine regulation of human growth JF - Acta paediatrica : nurturing the child N2 - Aim Growth is a multifarious phenomenon that has been studied by nutritionists, economists, paediatric endocrinologists; archaeologists, child psychologists and other experts. Yet, a unifying theory of understanding growth regulation is still lacking. Method Critical review of the literature. Results We summarise evidence linking social competition and its effect on hierarchies in social structures, with the neuronal networks of the ventromedial hypothalamus and body size. The endocrine signalling system regulating growth hormone, Insulin-like-Growth-Factor1 and skeletal growth, is well conserved in the evolution of vertebrata for some 400 million years. The link between size and status permits adaptive plasticity, competitive growth and strategic growth adjustments also in humans. Humans perceive size as a signal of dominance with tallness being favoured and particularly prevalent in the upper social classes. Conclusion Westernised societies are competitive. People are tall, and "open to change." Social values include striving for status and prestige implying socio-economic domination. We consider the transition of political and social values following revolutions and civil wars, as key elements that interact with the evolutionarily conserved neuroendocrine competence for adaptive developmental plasticity, overstimulate the hypothalamic growth regulation and finally lead to the recent historic increases in average height. KW - competitive growth KW - developmental plasticity KW - evolution KW - growth KW - hormone-releasing hormone KW - strategic growth adjustments Y1 - 2022 U6 - https://doi.org/10.1111/apa.16504 SN - 0803-5253 SN - 1651-2227 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Baunach, Martin A1 - Chowdhury, Somak A1 - Stallforth, Pierre A1 - Dittmann-Thünemann, Elke T1 - The landscape of recombination events that create nonribosomal peptide diversity JF - Molecular biology and evolution : MBE N2 - Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches. KW - evolution KW - recombination KW - structural diversity KW - natural products KW - nonribosomal peptide synthetases KW - microbial ecology Y1 - 2021 U6 - https://doi.org/10.1093/molbev/msab015 SN - 0737-4038 SN - 1537-1719 VL - 38 IS - 5 SP - 2116 EP - 2130 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Gonzalez Duran, Enrique T1 - Genetic control of intracellular gene transfer by DNA repair in N. tabacum N2 - Mitochondria and plastids are organelles with an endosymbiotic origin. During evolution, many genes are lost from the organellar genomes and get integrated in the nuclear genome, in what is known as intracellular/endosymbiotic gene transfer (IGT/EGT). IGT has been reproduced experimentally in Nicotiana tabacum at a gene transfer rate (GTR) of 1 event in 5 million cells, but, despite its centrality to eukaryotic evolution, there are no genetic factors known to influence the frequency of IGT in higher eukaryotes. The focus of this work was to determine the role of different DNA repair pathways of double strand break repair (DSBR) in the integration step of organellar DNA in the nuclear genome during IGT. Here, a CRISPR/Cas9 mutagenesis strategy was implemented in N. tabacum, with the aim of generating mutants in nuclear genes without expected visible phenotypes. This strategy led to the generation of a collection of independent mutants in the LIG4 (necessary for non-homologous end joining, NHEJ) and POLQ genes (necessary for microhomology mediated end joining, MMEJ). Targeting of other DSBR genes (KU70, KU80, RPA1C) generated mutants with unexpectedly strong developmental phenotypes.. These factors have telomeric roles, hinting towards a possible relationship between telomere length, and strength of developmental disruption upon loss of telomere structure in plants. The mutants were made in a genetic background encoding a plastid-encoded IGT reporter, that confers kanamycin resistance upon transfer to the nucleus. Through large scale independent experiments, increased IGT from the chloroplast to the nucleus was observed in lig4 mutants, as well as lines encoding a POLQ gene with a defective polymerase domain (polqΔPol). This shows that NHEJ or MMEJ have a double-sided relationship with IGT: while transferred genes may integrate using either pathway, the presence of both pathways suppresses IGT in wild-type somatic cells, thus demonstrating for the first time the extent on which nuclear genes control IGT frequency in plants. The IGT frequency increases in the mutants are likely mediated by increased availability of double strand breaks for integration. Additionally, kinetic analysis reveals that gene transfer (GT) events accumulate linearly as a function of time spent under antibiotic selection in the experiment, demonstrating that, contrary to what was previously thought, there is no such thing as a single GTR in somatic IGT experiments. Furthermore, IGT in tissue culture experiments appears to be the result of a "race against the clock" for integration in the nuclear genome, that starts when the organellar DNA arrives to the nucleus granting transient antibiotic resistance. GT events and escapes of kanamycin selection may be two possible outcomes from this race: those instances where the organellar DNA gets to integrate are recovered as GT events, and in those cases where timely integration fails, antibiotic resistance cannot be sustained, and end up considered as escapes. In the mutants, increased opportunities for integration in the nuclear genome change the overall ratio between IGT and escape events. The resources generated here are promising starting points for future research: (1) the mutant collection, for the further study of processes that depend on DNA repair in plants (2) the collection of GT lines obtained from these experiments, for the study of the effect of DSBR pathways over integration patterns and stability of transferred genes and (3) the developed CRISPR/Cas9 workflow for mutant generation, to make N. tabacum meet its potential as an attractive model for answering complex biological questions. N2 - Mitochondrien und Plastiden sind beides Organellen endosymbiotischen Ursprungs. Im Laufe der Evolution gehen viele Gene aus den Organellengenomen verloren und werden in das Kerngenom integriert, was als intrazellulärer/endosymbiotischer Gentransfer (IGT/EGT) bezeichnet wird. IGT konnte experimentell in Nicotiana tabacum mit einer Gentransferrate (GTR) von einem Ereignis in fünf Millionen Zellen nachgestellt werden, aber trotz seiner zentralen Bedeutung für die eukaryotische Evolution sind keine genetischen Faktoren bekannt, die die Häufigkeit von IGT in höheren Eukaryoten beeinflussen. Der Schwerpunkt dieser Arbeit lag auf der Bestimmung der Rolle verschiedener DNA-Reparaturwege der Doppelstrangbruchreparatur (DSBR) bei der Integration von Organellen-DNA in das Kerngenom während des IGT. Dazu wurde in N. tabacum eine CRISPR/Cas9-basierte Mutagenesestrategie angewandt, mit dem Ziel, Mutanten in Kerngenen zu erzeugen, für die keine sichtbaren Phänotypen zu erwarten sind. Diese Strategie führte zur Erzeugung einer Reihe unabhängiger Mutanten im LIG4-Gen (notwendig für „non-homologous end joining“, die nicht-homologe Verbindung von Enden, NHEJ) und POLQ (notwendig für „microhomology mediated end joining“, die Mikrohomologie-vermittelte Verbindung von Enden, MMEJ). Die gezielte Beeinflussung anderer DSBR-Gene (KU70, KU80, RPA1C) führte zu Mutanten mit unerwartet starken Entwicklungsphänotypen. Diese Gene spielen eine Rolle beim Erhalt der Telomere, was auf einen möglichen Zusammenhang zwischen der Telomerlänge und der Stärke der Entwicklungsstörung bei Verlust der Telomerstruktur in Pflanzen hindeutet. Die Mutanten wurden in einem genetischen Hintergrund erzeugt, der über einen in den Plastiden lokalisierten IGT-Reporter verfügt, der nach Übertragung in den Zellkern Kanamycin-Resistenz vermittelt. In groß angelegten unabhängigen Experimenten wurde in lig4-Mutanten sowie in Linien, die für ein POLQ-Gen mit einer defekten Polymerase-Domäne (polqΔPol) kodieren, eine erhöhte GTR vom Chloroplasten zum Zellkern beobachtet. Dies zeigt, dass NHEJ oder MMEJ eine zweischneidige Beziehung zum IGT haben: Während übertragene Gene folglich über jeden der beiden Mechanismen integriert werden können, unterdrückt das gleichzeitige Vorhandensein beider Wege IGT in somatischen Wildtyp-Zellen, wodurch zum ersten Mal gezeigt wird, in welchem Ausmaß Kerngene die IGT-Häufigkeit in Pflanzen kontrollieren. Die erhöhte Verfügbarkeit von Doppelstrangbrüchen für die Integration könnte für die erhöhte IGT-Häufigkeit in den Mutanten verantwortlich sein. Darüber hinaus zeigt die Analyse des Zeitverlaufs, dass Gentransferereignisse (GT) in Abhängigkeit von der Zeit, die im Experiment unter Antibiotikaselektion verbracht wurde, linear akkumulieren, was beweist, dass es, anders als bisher angenommen, in somatischen IGT-Experimenten keine statische GTR gibt. Darüber hinaus scheint IGT in Gewebekulturexperimenten das Ergebnis eines Wettlaufs mit der Zeit um die Integration in das Kerngenom zu sein, der beginnt, wenn die Organellen-DNA in den Zellkern gelangt und eine vorübergehende Antibiotikaresistenz gewährt. Echte GT-Ereignisse und „Escapes“ (scheinbare Resistenz, ein vorläufiges Ausweichen vor der Kanamycin-Selektion) können zwei mögliche Ergebnisse dieses Wettlaufs sein: Die Fälle, in denen die Organellen-DNA integriert wird, werden als GT-Ereignisse gewertet, und in den Fällen, in denen die rechtzeitige Integration scheitert, kann die Antibiotikaresistenz nicht aufrechterhalten werden und sie werden als „Escape“ betrachtet. In den Mutanten verändern sich die Möglichkeiten zur Integration in das Kerngenom, wodurch sich das Gesamtverhältnis zwischen IGT- und „Escape“-Ereignissen ändert. Die hier erzeugten Ressourcen sind vielversprechende Ausgangspunkte für künftige Forschungen: (1) die Mutantensammlung, für die Untersuchung von weiteren Prozessen, die von der DNA-Reparatur in Pflanzen abhängen, (2) die Sammlung von GT-Linien, die aus den hier beschriebenen Experimenten gewonnen wurden, für die Untersuchung der Auswirkungen von DSBR-Mechanismen auf Integrationsmuster und Stabilität übertragener Gene und (3) der hier entwickelte Arbeitsablauf für die Mutantenerzeugung mittels CRISPR/Cas9, damit N. tabacum sein Potenzial als attraktives Modell für die Beantwortung komplexer biologischer Fragestellungen erfüllen kann. T2 - Genetische Kontrolle des intrazellulären Gentransfers durch DNA-Reparatur in N. tabacum KW - endosymbiosis KW - organelles KW - gene KW - transfer KW - DNA KW - repair KW - genome KW - editing KW - evolution KW - plant Y1 - 2023 ER - TY - JOUR A1 - Lenzner, Bernd A1 - Magallon, Susana A1 - Dawson, Wayne A1 - Kreft, Holger A1 - König, Christian A1 - Pergl, Jan A1 - Pysek, Petr A1 - Weigelt, Patrick A1 - van Kleunen, Mark A1 - Winter, Marten A1 - Dullinger, Stefan A1 - Essl, Franz T1 - Role of diversification rates and evolutionary history as a driver of plant naturalization success JF - New phytologist : international journal of plant science N2 - Human introductions of species beyond their natural ranges and their subsequent establishment are defining features of global environmental change. However, naturalized plants are not uniformly distributed across phylogenetic lineages, with some families contributing disproportionately more to the global alien species pool than others. Additionally, lineages differ in diversification rates, and high diversification rates have been associated with characteristics that increase species naturalization success. Here, we investigate the role of diversification rates in explaining the naturalization success of angiosperm plant families. We use five global data sets that include native and alien plant species distribution, horticultural use of plants, and a time-calibrated angiosperm phylogeny. Using phylogenetic generalized linear mixed models, we analysed the effect of diversification rate, different geographical range measures, and horticultural use on the naturalization success of plant families. We show that a family's naturalization success is positively associated with its evolutionary history, native range size, and economic use. Investigating interactive effects of these predictors shows that native range size and geographic distribution additionally affect naturalization success. High diversification rates and large ranges increase naturalization success, especially of temperate families. We suggest this may result from lower ecological specialization in temperate families with large ranges, compared with tropical families with smaller ranges. KW - alien species KW - evolution KW - geographic distribution KW - invasion success KW - plant naturalization KW - range size Y1 - 2020 U6 - https://doi.org/10.1111/nph.17014 SN - 0028-646X SN - 1469-8137 VL - 229 IS - 5 SP - 2998 EP - 3008 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ehrlich, Elias A1 - Kath, Nadja Jeanette A1 - Gaedke, Ursula T1 - The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton JF - The ISME journal N2 - Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change. KW - coexistence KW - community ecology KW - diversity KW - evolution KW - fitness KW - functional traits KW - lake KW - maintenance KW - mechanisms KW - plankton Y1 - 2020 U6 - https://doi.org/10.1038/s41396-020-0619-1 SN - 1751-7362 SN - 1751-7370 VL - 14 IS - 6 SP - 1451 EP - 1462 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Westbury, Michael V. A1 - Hartmann, Stefanie A1 - Barlow, Axel A1 - Wiesel, Ingrid A1 - Leo, Viyanna A1 - Welch, Rebecca A1 - Parker, Daniel M. A1 - Sicks, Florian A1 - Ludwig, Arne A1 - Dalen, Love A1 - Hofreiter, Michael T1 - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena JF - Molecular biology and evolution N2 - Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species. KW - evolution KW - hyena KW - genomics KW - population genomics KW - diversity Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy037 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 5 SP - 1225 EP - 1237 PB - Oxford Univ. Press CY - Oxford ER -