TY - JOUR A1 - Nguyen, Hung M. A1 - Schippers, Jos H. M. A1 - Goni-Ramos, Oscar A1 - Christoph, Mathias P. A1 - Dortay, Hakan A1 - van der Hoorn, Renier A. L. A1 - Müller-Röber, Bernd T1 - An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana JF - The plant journal N2 - In both animal and plant kingdoms, body size is a fundamental but still poorly understood attribute of biological systems. Here we report that the Arabidopsis NAC transcription factor Regulator of Proteasomal Gene Expression' (RPX) controls leaf size by positively modulating proteasome activity. We further show that the cis-element recognized by RPX is evolutionarily conserved between higher plant species. Upon over-expression of RPX, plants exhibit reduced growth, which may be reversed by a low concentration of the pharmacological proteasome inhibitor MG132. These data suggest that the rate of protein turnover during growth is a critical parameter for determining final organ size. KW - Arabidopsis thaliana KW - organ size KW - evolution KW - leaf development KW - proteasome KW - gene regulatory network Y1 - 2013 U6 - https://doi.org/10.1111/tpj.12097 SN - 0960-7412 VL - 74 IS - 1 SP - 25 EP - 36 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Naujokat, Stefan A1 - Neubauer, Johannes A1 - Lamprecht, Anna-Lena A1 - Steffen, Bernhard A1 - Joerges, Sven A1 - Margaria, Tiziana T1 - Simplicity-first model-based plug-in development JF - Software : practice & experience N2 - In this article, we present our experience with over a decade of strict simplicity orientation in the development and evolution of plug-ins. The point of our approach is to enable our graphical modeling framework jABC to capture plug-in development in a domain-specific setting. The typically quite tedious and technical plug-in development is shifted this way from a programming task to the modeling level, where it can be mastered also by application experts without programming expertise. We show how the classical plug-in development profits from a systematic domain-specific API design and how the level of abstraction achieved this way can be further enhanced by defining adequate building blocks for high-level plug-in modeling. As the resulting plug-in models can be compiled and deployed automatically, our approach decomposes plug-in development into three phases where only the realization phase requires plug-in-specific effort. By using our modeling framework jABC, this effort boils down to graphical, tool-supported process modeling. Furthermore, we support the automatic completion of process sketches for executability. All this will be illustrated along the most recent plug-in-based evolution of the jABC framework, which witnessed quite some bootstrapping effects. KW - plug-ins KW - simplicity KW - domain-specific APIs KW - process modeling KW - bootstrapping KW - evolution KW - code generation KW - loose programming KW - dynamic service binding Y1 - 2014 U6 - https://doi.org/10.1002/spe.2243 SN - 0038-0644 SN - 1097-024X VL - 44 IS - 3 SP - 277 EP - 297 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Zancolli, Giulia A1 - Baker, Timothy G. A1 - Barlow, Axel A1 - Bradley, Rebecca K. A1 - Calvete, Juan J. A1 - Carter, Kimberley C. A1 - de Jager, Kaylah A1 - Owens, John Benjamin A1 - Price, Jenny Forrester A1 - Sanz, Libia A1 - Scholes-Higham, Amy A1 - Shier, Liam A1 - Wood, Liam A1 - Wüster, Catharine E. A1 - Wüster, Wolfgang T1 - Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus x viridis Hybrid Zone in Southwestern New Mexico JF - Toxins N2 - Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. KW - adaptation KW - Crotalus KW - evolution KW - hybridization KW - introgression KW - Mojave toxin KW - molecular evolution KW - venom Y1 - 2016 U6 - https://doi.org/10.3390/toxins8060188 SN - 2072-6651 VL - 8 PB - MDPI CY - Basel 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 - TY - JOUR A1 - Lozada Gobilard, Sissi Donna A1 - Weigend, M. A1 - Fischer, E. A1 - Janssens, S. B. A1 - Ackermann, M. A1 - Abrahamczyk, Stefan T1 - Breeding systems in Balsaminaceae in relation to pollen/ovule ratio, pollination syndromes, life history and climate zone JF - Plant biology N2 - Pollen/ovule (P/O) ratios are often used as proxy for breeding systems. Here, we investigate the relations between breeding systems and P/O ratios, pollination syndromes, life history and climate zone in Balsaminaceae. We conducted controlled breeding system experiments (autonomous and active self-pollination and outcrossing tests) for 65 Balsaminaceae species, analysed pollen grain and ovule numbers and evaluated the results in combination with data on pollination syndrome, life history and climate zone on a phylogenetic basis. Based on fruit set, we assigned three breeding systems: autogamy, self-compatibility and self-incompatibility. Self-pollination led to lower fruit set than outcrossing. We neither found significant P/O differences between breeding systems nor between pollination syndromes. However, the numbers of pollen grains and ovules per flower were significantly lower in autogamous species, but pollen grain and ovule numbers did not differ between most pollination syndromes. Finally, we found no relation between breeding system and climate zone, but a relation between climate zone and life history. In Balsaminaceae reproductive traits can change under resource or pollinator limitation, leading to the evolution of autogamy, but are evolutionary rather constant and not under strong selection pressure by pollinator guild and geographic range changes. Colonisation of temperate regions, however, is correlated with transitions towards annual life history. Pollen/ovule-ratios, commonly accepted as good indicators of breeding system, have a low predictive value in Balsaminaceae. In the absence of experimental data on breeding system, additional floral traits (overall pollen grain and ovule number, traits of floral morphology) may be used as proxies. KW - Annual KW - autogamy KW - cleistogamy KW - evolution KW - fly pollination KW - Impatiens KW - outcrossing KW - perennial KW - self-incompatibility KW - temperate KW - tropical Y1 - 2018 U6 - https://doi.org/10.1111/plb.12905 SN - 1435-8603 SN - 1438-8677 VL - 21 IS - 1 SP - 157 EP - 166 PB - Wiley CY - Hoboken 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 - 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 - 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 -