TY - GEN AB - Data underlying the figures in the publication "The chemistry of Cu3N and Cu3PdN nanocrystals" AU - Parvizian, Mahsa AU - Duran Balsa, Alejandra AU - Pokratath, Rohan AU - Kalha, Curran AU - Lee, Seungho AU - Van den Eynden, Dietger AU - Ibáñez, Maria AU - Regoutz, Anna AU - De Roo, Jonathan ID - 11695 TI - Data for "The chemistry of Cu3N and Cu3PdN nanocrystals" ER - TY - GEN AB - Codes and data for reproducing the results of N. B. Budanur and B. Hof "An autonomous compartmental model for accelerating epidemics" AU - Budanur, Nazmi B ID - 11711 TI - burakbudanur/autoacc-public ER - TY - GEN AB - Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies. AU - Orliac, Etienne AU - Trejo Banos, Daniel AU - Ojavee, Sven AU - Läll, Kristi AU - Mägi, Reedik AU - Visscher, Peter AU - Robinson, Matthew Richard ID - 13064 TI - Improving genome-wide association discovery and genomic prediction accuracy in biobank data ER - TY - GEN AB - Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales. AU - Tomanek, Isabella AU - Guet, Calin C ID - 12339 TI - Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose ER - TY - GEN AB - Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence. AU - Koch, Eva AU - Ravinet, Mark AU - Westram, Anja M AU - Jonannesson, Kerstin AU - Butlin, Roger ID - 13066 TI - Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution ER - TY - GEN AB - This dataset comprises all data shown in the figures of the submitted article "Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request. AU - Zemlicka, Martin AU - Redchenko, Elena AU - Peruzzo, Matilda AU - Hassani, Farid AU - Trioni, Andrea AU - Barzanjeh, Shabir AU - Fink, Johannes M ID - 14520 TI - Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses ER - TY - DATA AB - FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. AU - Radler, Philipp ID - 10934 KW - Bacterial cell division KW - in vitro reconstitution KW - FtsZ KW - FtsN KW - FtsA TI - In vitro reconstitution of Escherichia coli divisome activation ER - TY - DATA AU - Schulz, Rouven ID - 11542 TI - Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses) ER - TY - DATA AB - This .zip File contains the transport data, the codes for the data analysis, the microscopy analysis and the codes for the theoretical simulations for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks" by M. Valentini, et. al. The transport data are saved with hdf5 file format. The files can be open with the log browser of Labber. AU - Valentini, Marco AU - San-Jose, Pablo AU - Arbiol, Jordi AU - Marti-Sanchez, Sara AU - Botifoll, Marc ID - 12522 TI - Data for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks" ER - TY - DATA AB - Here are the research data underlying the publication "Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus" Further information are summed up in the README document. AU - Surendranadh, Parvathy AU - Arathoon, Louise S AU - Baskett, Carina AU - Field, David AU - Pickup, Melinda AU - Barton, Nicholas H ID - 11321 TI - Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus ER - TY - DATA AB - Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality. AU - Elkrewi, Marwan N ID - 11653 TI - Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp" ER - TY - GEN AB - CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits) AU - McCartney, Daniel L AU - Hillary, Robert F AU - Conole, Eleanor LS AU - Trejo Banos, Daniel AU - Gadd, Danni A AU - Walker, Rosie M AU - Nangle, Cliff AU - Flaig, Robin AU - Campbell, Archie AU - Murray, Alison D AU - Munoz Maniega, Susana AU - del C Valdes-Hernandez, Maria AU - Harris, Mathew A AU - Bastin, Mark E AU - Wardlaw, Joanna M AU - Harris, Sarah E AU - Porteous, David J AU - Tucker-Drob, Elliot M AU - McIntosh, Andrew M AU - Evans, Kathryn L AU - Deary, Ian J AU - Cox, Simon R AU - Robinson, Matthew Richard AU - Marioni, Riccardo E ID - 13072 TI - Blood-based epigenome-wide analyses of cognitive abilities ER - TY - GEN AB - Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids". AU - Randriamanantsoa, Samuel AU - Papargyriou, Aristeidis AU - Maurer, Carlo AU - Peschke, Katja AU - Schuster, Maximilian AU - Zecchin, Giulia AU - Steiger, Katja AU - Öllinger, Rupert AU - Saur, Dieter AU - Scheel, Christina AU - Rad, Roland AU - Hannezo, Edouard B AU - Reichert, Maximilian AU - Bausch, Andreas R. ID - 13068 TI - Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids ER - TY - GEN AB - Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome. AU - Koch, Eva AU - Morales, Hernán E. AU - Larsson, Jenny AU - Westram, Anja M AU - Faria, Rui AU - Lemmon, Alan R. AU - Lemmon, E. Moriarty AU - Johannesson, Kerstin AU - Butlin, Roger K. ID - 12987 TI - Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis ER - TY - GEN AB - Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org)) We upload a pdf with extended data sets, and the raw data for these extended datasets as well. AU - Puglia, Denise AU - Martinez, Esteban AU - Menard, Gerbold AU - Pöschl, Andreas AU - Gronin, Sergei AU - Gardner, Geoffrey AU - Kallaher, Ray AU - Manfra, Michael AU - Marcus, Charles AU - Higginbotham, Andrew P AU - Casparis, Lucas ID - 13080 TI - Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire ER - TY - GEN AB - This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request. AU - Peruzzo, Matilda AU - Hassani, Farid AU - Szep, Grisha AU - Trioni, Andrea AU - Redchenko, Elena AU - Zemlicka, Martin AU - Fink, Johannes M ID - 13057 TI - Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction ER - TY - GEN AB - Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism. AU - Casillas Perez, Barbara E AU - Pull, Christopher AU - Naiser, Filip AU - Naderlinger, Elisabeth AU - Matas, Jiri AU - Cremer, Sylvia ID - 13061 TI - Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies ER - TY - GEN AB - To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal. AU - Chauve, Laetitia AU - Hodge, Francesca AU - Murdoch, Sharlene AU - Masoudzadeh, Fatemah AU - Mann, Harry-Jack AU - Lopez-Clavijo, Andrea AU - Okkenhaug, Hanneke AU - West, Greg AU - Sousa, Bebiana C. AU - Segonds-Pichon, Anne AU - Li, Cheryl AU - Wingett, Steven AU - Kienberger, Hermine AU - Kleigrewe, Karin AU - de Bono, Mario AU - Wakelam, Michael AU - Casanueva, Olivia ID - 13069 TI - Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans ER - TY - GEN AB - The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt. AU - Ucar, Mehmet C ID - 13058 TI - Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance" ER - TY - GEN AB - This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments. AU - Szep, Eniko AU - Sachdeva, Himani AU - Barton, Nicholas H ID - 13062 TI - Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model ER - TY - GEN AB - We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data. AU - Robinson, Matthew Richard ID - 13063 TI - Probabilistic inference of the genetic architecture of functional enrichment of complex traits ER - TY - GEN AB - Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS AU - Johnson, Alexander J ID - 14988 TI - Raw data from Johnson et al, PNAS, 2021 ER - TY - DATA AB - This .zip File contains the transport data for figures presented in the main text and supplementary material of "Enhancement of Proximity Induced Superconductivity in Planar Germanium" by K. Aggarwal, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). AU - Katsaros, Georgios ID - 9291 TI - Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium ER - TY - DATA AU - Higginbotham, Andrew P ID - 9636 TI - Data for "Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid" ER - TY - DATA AB - This .zip File contains the data for figures presented in the main text and supplementary material of "A singlet triplet hole spin qubit in planar Ge" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python. AU - Jirovec, Daniel ID - 9323 TI - Research data for "A singlet-triplet hole spin qubit planar Ge" ER - TY - DATA AB - This .zip File contains the transport data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states" by M. Valentini, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. Instructions of how to read the data are in "Notebook_Valentini.pdf". AU - Valentini, Marco ID - 9389 TI - Research data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states" ER - TY - DATA AB - Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)." Further information are summed up in the README document. AU - Surendranadh, Parvathy AU - Arathoon, Louise S AU - Baskett, Carina AU - Field, David AU - Pickup, Melinda AU - Barton, Nicholas H ID - 9192 TI - Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus ER - TY - DATA AU - Vicoso, Beatriz ID - 9949 TI - Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of gene expression in Artemia brine shrimp" ER - TY - GEN AB - The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact. AU - Simon, Alexis AU - Fraisse, Christelle AU - El Ayari, Tahani AU - Liautard-Haag, Cathy AU - Strelkov, Petr AU - Welch, John AU - Bierne, Nicolas ID - 13073 TI - How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels ER - TY - GEN AB - Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available. AU - Arnoux, Stephanie AU - Fraisse, Christelle AU - Sauvage, Christopher ID - 13065 TI - VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species ER - TY - GEN AB - Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP) AU - Ucar, Mehmet C AU - Lipowsky, Reinhard ID - 9885 TI - MURL_Dataz ER - TY - GEN AU - Grah, Rok AU - Friedlander, Tamar ID - 9779 TI - Distribution of crosstalk values ER - TY - GEN AU - Grah, Rok AU - Friedlander, Tamar ID - 9776 TI - Supporting information ER - TY - GEN AB - This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided. AU - Hartstein, Mate AU - Hsu, Yu-Te AU - Modic, Kimberly A AU - Porras, Juan AU - Loew, Toshinao AU - Le Tacon, Matthieu AU - Zuo, Huakun AU - Wang, Jinhua AU - Zhu, Zengwei AU - Chan, Mun AU - McDonald, Ross AU - Lonzarich, Gilbert AU - Keimer, Bernhard AU - Sebastian, Suchitra AU - Harrison, Neil ID - 9708 TI - Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors' ER - TY - GEN AB - When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. AU - Perini, Samuel AU - Rafajlovic, Marina AU - Westram, Anja M AU - Johannesson, Kerstin AU - Butlin, Roger ID - 8809 TI - Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina ER - TY - GEN AB - The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I. AU - Gupta, Chitrak AU - Khaniya, Umesh AU - Chan, Chun AU - Dehez, Francois AU - Shekhar, Mrinal AU - Gunner, M. R. AU - Sazanov, Leonid A AU - Chipot, Christophe AU - Singharoy, Abhishek ID - 9326 TI - Charge transfer and chemo-mechanical coupling in respiratory complex I ER - TY - GEN AB - Additional analyses of the trajectories AU - Gupta, Chitrak AU - Khaniya, Umesh AU - Chan, Chun Kit AU - Dehez, Francois AU - Shekhar, Mrinal AU - Gunner, M.R. AU - Sazanov, Leonid A AU - Chipot, Christophe AU - Singharoy, Abhishek ID - 9713 TI - Supporting information ER - TY - GEN AU - Gupta, Chitrak AU - Khaniya, Umesh AU - Chan, Chun Kit AU - Dehez, Francois AU - Shekhar, Mrinal AU - Gunner, M.R. AU - Sazanov, Leonid A AU - Chipot, Christophe AU - Singharoy, Abhishek ID - 9878 TI - Movies ER - TY - GEN AB - Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19). AU - Hillary, Robert F. AU - Trejo-Banos, Daniel AU - Kousathanas, Athanasios AU - McCartney, Daniel L. AU - Harris, Sarah E. AU - Stevenson, Anna J. AU - Patxot, Marion AU - Ojavee, Sven Erik AU - Zhang, Qian AU - Liewald, David C. AU - Ritchie, Craig W. AU - Evans, Kathryn L. AU - Tucker-Drob, Elliot M. AU - Wray, Naomi R. AU - McRae, Allan F. AU - Visscher, Peter M. AU - Deary, Ian J. AU - Robinson, Matthew Richard AU - Marioni, Riccardo E. ID - 9706 TI - Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults ER - TY - GEN AB - This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request. AU - Arnold, Georg M AU - Wulf, Matthias AU - Barzanjeh, Shabir AU - Redchenko, Elena AU - Rueda Sanchez, Alfredo R AU - Hease, William J AU - Hassani, Farid AU - Fink, Johannes M ID - 13056 TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface ER - TY - GEN AB - This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request. AU - Peruzzo, Matilda AU - Trioni, Andrea AU - Hassani, Farid AU - Zemlicka, Martin AU - Fink, Johannes M ID - 13070 TI - Surpassing the resistance quantum with a geometric superinductor ER - TY - GEN AB - This dataset comprises all data shown in the plots of the main part of the submitted article "Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State". Additional raw data are available from the corresponding author on reasonable request. AU - Hease, William J AU - Rueda Sanchez, Alfredo R AU - Sahu, Rishabh AU - Wulf, Matthias AU - Arnold, Georg M AU - Schwefel, Harald AU - Fink, Johannes M ID - 13071 TI - Bidirectional electro-optic wavelength conversion in the quantum ground state ER - TY - GEN AB - Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. AU - Fraisse, Christelle AU - Welch, John J. ID - 9799 TI - Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes ER - TY - GEN AB - Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. AU - Fraisse, Christelle AU - Welch, John J. ID - 9798 TI - Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes ER - TY - GEN AB - Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level. AU - Milutinovic, Barbara AU - Stock, Miriam AU - Grasse, Anna V AU - Naderlinger, Elisabeth AU - Hilbe, Christian AU - Cremer, Sylvia ID - 13060 TI - Social immunity modulates competition between coinfecting pathogens ER - TY - GEN AB - PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol Space Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90° AU - Schlemmer, Werner AU - Nothdurft, Philipp AU - Petzold, Alina AU - Riess, Gisbert AU - Frühwirt, Philipp AU - Schmallegger, Max AU - Gescheidt-Demner, Georg AU - Fischer, Roland AU - Freunberger, Stefan Alexander AU - Kern, Wolfgang AU - Spirk, Stefan ID - 9780 TI - CCDC 1991959: Experimental Crystal Structure Determination ER - TY - GEN AU - Grah, Rok AU - Friedlander, Tamar ID - 9777 TI - Maximizing crosstalk ER - TY - GEN AB - Data and mathematica notebooks for plotting figures from Language learning with communication between learners AU - Ibsen-Jensen, Rasmus AU - Tkadlec, Josef AU - Chatterjee, Krishnendu AU - Nowak, Martin ID - 9814 TI - Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners ER - TY - DATA AB - This data collection contains the transport data for figures presented in the supplementary material of "Enhancement of Proximity Induced Superconductivity in Planar Germanium" by K. Aggarwal, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). AU - Katsaros, Georgios ID - 8834 TI - Enhancement of proximity induced superconductivity in planar Germanium ER - TY - DATA AB - Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology. AU - Kavcic, Bor ID - 8097 KW - Escherichia coli KW - antibiotic combinations KW - translation KW - growth laws KW - drug interactions KW - bacterial physiology KW - translation inhibitors TI - Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics" ER - TY - DATA AB - Here are the research data underlying the publication "Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)". Further information are summed up in the README document. The files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192. AU - Arathoon, Louise S ID - 8254 TI - Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus) ER - TY - DATA AB - Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems. AU - Kavcic, Bor ID - 8930 KW - Escherichia coli KW - antibiotic combinations KW - translation KW - growth laws KW - drug interactions KW - bacterial physiology KW - translation inhibitors TI - Analysis scripts and research data for the paper "Minimal biophysical model of combined antibiotic action" ER - TY - DATA AB - Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks. AU - Nagy-Staron, Anna A ID - 8951 KW - Gene regulatory networks KW - Gene expression KW - Escherichia coli KW - Synthetic Biology TI - Sequences of gene regulatory network permutations for the article "Local genetic context shapes the function of a gene regulatory network" ER - TY - DATA AB - Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature. AU - Grah, Rok ID - 7383 KW - Matlab scripts KW - analysis of microfluidics KW - mathematical model TI - Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation ER - TY - DATA AU - Katsaros, Georgios ID - 9222 TI - Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling ER - TY - DATA AB - Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape. AU - Guseinov, Ruslan ID - 8375 TI - Supplementary data for "Computational design of curved thin shells: from glass façades to programmable matter" ER - TY - DATA AB - These are the supplementary research data to the publication "Zero field splitting of heavy-hole states in quantum dots". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file. AU - Katsaros, Georgios ID - 7689 TI - Supplementary data for "Zero field splitting of heavy-hole states in quantum dots" ER - TY - DATA AU - Guseinov, Ruslan ID - 8761 TI - Supplementary data for "Computational design of cold bent glass façades" ER - TY - DATA AB - Supplementary data provided for the provided for the publication: Igor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife. AU - Csicsvari, Jozsef L AU - Gridchyn, Igor AU - Schönenberger, Philipp ID - 8563 TI - Optogenetic alteration of hippocampal network activity ER - TY - DATA AB - Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications. AU - Schur, Florian KM ID - 14592 TI - STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy ER - TY - GEN AB - Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures. AU - Antoniou, Michael N. AU - Nicolas, Armel AU - Mesnage, Robin AU - Biserni, Martina AU - Rao, Francesco V. AU - Martin, Cristina Vazquez ID - 9784 TI - MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells ER - TY - GEN AB - More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range. AU - Polechova, Jitka ID - 9839 TI - Data from: Is the sky the limit? On the expansion threshold of a species' range ER - TY - GEN AB - A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF) AU - Ucar, Mehmet C AU - Lipowsky, Reinhard ID - 9726 TI - Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding ER - TY - GEN AU - Merrill, Richard M. AU - Rastas, Pasi AU - Martin, Simon H. AU - Melo Hurtado, Maria C AU - Barker, Sarah AU - Davey, John AU - Mcmillan, W. Owen AU - Jiggins, Chris D. ID - 9801 TI - Raw behavioral data ER - TY - GEN AB - 1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific. AU - Kutzer, Megan AU - Kurtz, Joachim AU - Armitage, Sophie A.O. ID - 9806 TI - Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance ER - TY - GEN AU - Pokusaeva, Victoria AU - Usmanova, Dinara R. AU - Putintseva, Ekaterina V. AU - Espinar, Lorena AU - Sarkisyan, Karen AU - Mishin, Alexander S. AU - Bogatyreva, Natalya S. AU - Ivankov, Dmitry AU - Akopyan, Arseniy AU - Avvakumov, Sergey AU - Povolotskaya, Inna S. AU - Filion, Guillaume J. AU - Carey, Lucas B. AU - Kondrashov, Fyodor ID - 9790 TI - A statistical summary of segment libraries and sequencing results ER - TY - GEN AU - Pokusaeva, Victoria AU - Usmanova, Dinara R. AU - Putintseva, Ekaterina V. AU - Espinar, Lorena AU - Sarkisyan, Karen AU - Mishin, Alexander S. AU - Bogatyreva, Natalya S. AU - Ivankov, Dmitry AU - Akopyan, Arseniy AU - Povolotskaya, Inna S. AU - Filion, Guillaume J. AU - Carey, Lucas B. AU - Kondrashov, Fyodor ID - 9797 TI - A statistical summary of segment libraries and sequencing results ER - TY - GEN AU - Pokusaeva, Victoria AU - Usmanova, Dinara R. AU - Putintseva, Ekaterina V. AU - Espinar, Lorena AU - Sarkisyan, Karen AU - Mishin, Alexander S. AU - Bogatyreva, Natalya S. AU - Ivankov, Dmitry AU - Akopyan, Arseniy AU - Avvakumov, Sergey AU - Povolotskaya, Inna S. AU - Filion, Guillaume J. AU - Carey, Lucas B. AU - Kondrashov, Fyodor ID - 9789 TI - Multiple alignment of His3 orthologues ER - TY - GEN AB - Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response. AU - Castro, João Pl AU - Yancoskie, Michelle N. AU - Marchini, Marta AU - Belohlavy, Stefanie AU - Hiramatsu, Layla AU - Kučka, Marek AU - Beluch, William H. AU - Naumann, Ronald AU - Skuplik, Isabella AU - Cobb, John AU - Barton, Nicholas H AU - Rolian, Campbell AU - Chan, Yingguang Frank ID - 9804 TI - Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice ER - TY - GEN AB - This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed. AU - Sachdeva, Himani ID - 9802 TI - Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat ER - TY - GEN AU - Ruess, Jakob AU - Pleska, Maros AU - Guet, Calin C AU - Tkačik, Gašper ID - 9786 TI - Supporting text and results ER - TY - GEN AB - Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle. AU - Puixeu Sala, Gemma AU - Pickup, Melinda AU - Field, David AU - Barrett, Spencer C.H. ID - 9803 TI - Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics ER - TY - GEN AB - OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb) AU - Sigalova, Olga AU - Chaplin, Andrei AU - Bochkareva, Olga AU - Shelyakin, Pavel AU - Filaretov, Vsevolod AU - Akkuratov, Evgeny AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9731 TI - Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9783 TI - Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9897 TI - Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9890 TI - Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Distribution of OGs with mosaic phyletic patterns across species (all genomes). (CSV 10 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9892 TI - Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Summary of peripheral genesa phyletic patterns and tree concordance. (CSV 26 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9893 TI - Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9894 TI - Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Additional information on proteins from OG1. (CSV 30 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9895 TI - Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Summary of the analysed genomes. (CSV 24 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9896 TI - Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9898 TI - Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9901 TI - Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9899 TI - Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Pan-genome statistics by species. (CSV 3 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9900 TI - Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females. AU - Johannesson, Kerstin AU - Zagrodzka, Zuzanna AU - Faria, Rui AU - Westram, Anja M AU - Butlin, Roger ID - 13067 TI - Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? ER - TY - GEN AB - The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event? AU - Barton, Nicholas H ID - 9805 TI - Data from: The consequences of an introgression event ER - TY - DATA AB - Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature. AU - Tomanek, Isabella ID - 7016 KW - Escherichia coli KW - gene amplification KW - galactose KW - DOG KW - experimental evolution KW - Illumina sequence data KW - FACS data KW - microfluidics data TI - Data for the paper "Gene amplification as a form of population-level gene expression regulation" ER - TY - DATA AU - Guseinov, Ruslan ID - 7154 TI - Supplementary data for "Programming temporal morphing of self-actuated shells" ER - TY - DATA AU - Vicoso, Beatriz ID - 6060 TI - Supplementary data for "Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). ER - TY - DATA AB - This dataset contains the supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition". The contained files have the following content: 'Supplementary Figures.pdf' Additional figures (as referenced in the paper). 'Supplementary Table 1. Statistics.xlsx' Details on statistical tests performed in the paper. 'Supplementary Table 2. Differentially expressed gene analysis.xlsx' Results for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples. 'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx' Results for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down). 'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx' Results for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant. 'Supplementary Table 5. Cluster identification.xlsx' Results for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories). 'Supplementary Table 6. GO term cluster analysis.xlsx' Results for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1). 'Supplementary Table 7. Setd5 mass spectrometry results.xlsx' Results showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma. 'Supplementary Table 8. PolII ChIP-seq analysis.xlsx' Results for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS. AU - Dotter, Christoph AU - Novarino, Gaia ID - 6074 TI - Supplementary data for the research paper "Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition" ER - TY - DATA AB - Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7). AU - Nardin, Michele ID - 6062 TI - Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals" ER - TY - GEN AB - Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients. AU - Faria, Rui AU - Chaube, Pragya AU - Morales, Hernán E. AU - Larsson, Tomas AU - Lemmon, Alan R. AU - Lemmon, Emily M. AU - Rafajlović, Marina AU - Panova, Marina AU - Ravinet, Mark AU - Johannesson, Kerstin AU - Westram, Anja M AU - Butlin, Roger K. ID - 9837 TI - Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes ER - TY - GEN AB - This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled "Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method". It also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript. The repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`. For details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee). AU - Garriga, Edgar AU - di Tommaso, Paolo AU - Magis, Cedrik AU - Erb, Ionas AU - Mansouri, Leila AU - Baltzis, Athanasios AU - Laayouni, Hafid AU - Kondrashov, Fyodor AU - Floden, Evan AU - Notredame, Cedric ID - 13059 TI - Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method ER - TY - GEN AB - Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity. AU - Payne, Pavel AU - Geyrhofer, Lukas AU - Barton, Nicholas H AU - Bollback, Jonathan P ID - 9840 TI - Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations ER - TY - GEN AB - File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables. AU - Bod'ová, Katarína AU - Priklopil, Tadeas AU - Field, David AU - Barton, Nicholas H AU - Pickup, Melinda ID - 9813 TI - Supplemental material for Bodova et al., 2018 ER - TY - GEN AB - Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity. AU - Harrison, Mark C. AU - Jongepier, Evelien AU - Robertson, Hugh M. AU - Arning, Nicolas AU - Bitard-Feildel, Tristan AU - Chao, Hsu AU - Childers, Christopher P. AU - Dinh, Huyen AU - Doddapaneni, Harshavardhan AU - Dugan, Shannon AU - Gowin, Johannes AU - Greiner, Carolin AU - Han, Yi AU - Hu, Haofu AU - Hughes, Daniel S. T. AU - Huylmans, Ann K AU - Kemena, Carsten AU - Kremer, Lukas P. M. AU - Lee, Sandra L. AU - Lopez-Ezquerra, Alberto AU - Mallet, Ludovic AU - Monroy-Kuhn, Jose M. AU - Moser, Annabell AU - Murali, Shwetha C. AU - Muzny, Donna M. AU - Otani, Saria AU - Piulachs, Maria-Dolors AU - Poelchau, Monica AU - Qu, Jiaxin AU - Schaub, Florentine AU - Wada-Katsumata, Ayako AU - Worley, Kim C. AU - Xie, Qiaolin AU - Ylla, Guillem AU - Poulsen, Michael AU - Gibbs, Richard A. AU - Schal, Coby AU - Richards, Stephen AU - Belles, Xavier AU - Korb, Judith AU - Bornberg-Bauer, Erich ID - 9841 TI - Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality ER - TY - GEN AU - Chaudhry, Waqas AU - Pleska, Maros AU - Shah, Nilang AU - Weiss, Howard AU - Mccall, Ingrid AU - Meyer, Justin AU - Gupta, Animesh AU - Guet, Calin C AU - Levin, Bruce ID - 9810 TI - Numerical data used in figures ER - TY - GEN AB - This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb) AU - Zapata, Luis AU - Pich, Oriol AU - Serrano, Luis AU - Kondrashov, Fyodor AU - Ossowski, Stephan AU - Schaefer, Martin ID - 9812 TI - Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome ER - TY - GEN AB - This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb) AU - Zapata, Luis AU - Pich, Oriol AU - Serrano, Luis AU - Kondrashov, Fyodor AU - Ossowski, Stephan AU - Schaefer, Martin ID - 9811 TI - Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome ER -