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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Tanner, Alastair R.; Fuchs, Dirk; Winkelmann, Inger E.; Gilbert, Thomas P.; +9 Authors

    Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian–Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates. aligned_supermatrix_36156_x_52_phylipAligned supermatrix, 180 genes, 36,156 amino acid positions, 52 taxa. Phylip format.ceph_1aug_36156

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2017
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; NARCIS
    Dataset . 2017
    License: CC 0
    Data sources: Datacite; NARCIS
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2017
      License: CC 0
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; NARCIS
      Dataset . 2017
      License: CC 0
      Data sources: Datacite; NARCIS
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Rimington, William R.; Pressel, Silvia; Duckett, Jeffrey G.; Field, Katie J.; +2 Authors

    Arbuscular mycorrhizas are widespread in land plants including liverworts, some of the closest living relatives of the first plants to colonise land 500 MYA. Previous investigations reported near-exclusive colonisation of liverworts by the most recently evolved arbuscular mycorrhizal fungi, the Glomeraceae, indicating a recent acquisition from flowering plants at odds with the widely-held notion that arbuscular mycorrhizal-like associations in liverworts represent the ancestral symbiotic condition in land plants. We performed an analysis of symbiotic fungi in 674 globally-collected liverworts using molecular phylogenetics and electron microscopy. Here we show every order of arbuscular mycorrhizal fungi colonises early-diverging liverworts, with non-Glomeraceae being at least ten times more common than in flowering plants. Arbuscular mycorrhizal fungi in liverworts and other ancient plant lineages (hornworts, lycopods and ferns) were delimited into 58 taxa and 36 singletons, of which at least 43 are novel and specific to liverworts. The discovery that early plant lineages are colonised by early-diverging fungi supports the hypothesis that arbuscular mycorrhizas are an ancestral symbiosis for all land plants. Figure_1_alignmentAlignment of Glomeromycotina fungi sequences used to produce phylogenetic tree presented in Figure 1. Sequence alignment was performed using MUSCLE algorithms within MEGA7.Figure_1_treeMaximum likelihood phylogenetic tree of Glomeromycotina fungi that can be seen in Figure 1. Tree is in Newick format, having been produced in MEGA7 using the generalised time reversible model with invariant gamma rates and 1,000 bootstrap replicates.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Dataset . 2018
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; NARCIS
    Dataset . 2018
    License: CC 0
    Data sources: Datacite; NARCIS
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2018
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2018
      License: CC 0
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; NARCIS
      Dataset . 2018
      License: CC 0
      Data sources: Datacite; NARCIS
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2018
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Gomez-Llano, Miguel Angel; Navarro-López, Eva Maria; Gilman, Robert Tucker;

    Sexual imprinting is the learning of a mate preference by direct observation of the phenotype of another member of the population. Sexual imprinting can be paternal, maternal, or oblique if individuals learn to prefer the phenotypes of their fathers, mothers, or other members of the population, respectively. Which phenotypes are learned can affect trait evolution and speciation rates. “Good genes” models of polygynous systems predict that females should evolve to imprint on their fathers, because paternal imprinting helps females to choose mates that will produce offspring that are both viable and sexy. Sexual imprinting by males has been observed in nature, but a theory for the evolution of sexual imprinting by males does not exist. We developed a good genes model to study the conditions under which sexual imprinting by males or by both sexes can evolve and to ask which sexual imprinting strategies maximize the fitness of the choosy sex. We found that when only males imprint, maternal imprinting is the most advantageous strategy. When both sexes imprint, it is most advantageous for both sexes to use paternal imprinting. Previous theory suggests that, in a given population, either males or females but not both will evolve choosiness in mating. We show how environmental change can lead to the evolution of sexual imprinting behavior by both sexes in the same population. Vecor_fields

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2017
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; NARCIS
    Dataset . 2017
    License: CC 0
    Data sources: Datacite; NARCIS
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2017
      License: CC 0
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; NARCIS
      Dataset . 2017
      License: CC 0
      Data sources: Datacite; NARCIS
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Siveter, Derek J.; Briggs, Derek E. G.; Siveter, David J.; Sutton, Mark D.; +3 Authors

    A new arthropod, Enalikter aphson gen. et sp. nov., is described from the Silurian (Wenlock Series) Herefordshire Lagerstätte of the UK. It belongs to the Megacheira (=short-great-appendage group), which is recognized here, for the first time, in strata younger than mid-Cambrian age. Discovery of this new Silurian taxon allows us to identify a Devonian megacheiran representative, Bundenbachiellus giganteus from the Hunsrück Slate of Germany. The phylogenetic position of megacheirans is controversial: they have been interpreted as stem chelicerates, or stem euarthropods, but when Enalikter and Bundenbachiellus are added to the most comprehensive morphological database available, a stem euarthropod position is supported. Enalikter represents the only fully three-dimensionally preserved stem-group euarthropod, it falls in the sister clade to the crown-group euarthropods, and it provides new insights surrounding the origin and early evolution of the euarthropods. Recognition of Enalikter and Bundenbachiellus as megacheirans indicates that this major arthropod group survived for nearly 100 Myr beyond the mid-Cambrian. OUM C.29631Holotype of Enalikter aphson in VAXML format (see ReadMe file)OUM_C29631.zipOUM C.29632Specimen of Enalikter aphson in VAXML format (see ReadMe file)OUM_C29632.zipOUM C.29633Specimen of Enalikter aphson in VAXML format (see ReadMe file).OUM_C29633.zip

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    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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    DRYAD; NARCIS
    Dataset . 2015
    License: CC 0
    Data sources: Datacite; NARCIS
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    ZENODO
    Dataset . 2015
    License: CC 0
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
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      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
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      DRYAD; NARCIS
      Dataset . 2015
      License: CC 0
      Data sources: Datacite; NARCIS
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2015
      License: CC 0
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Keelan, Jonathan; Hague, James P.; Chung, Emma M. L.;

    Do the complex processes of angiogenesis during organism development ultimately lead to a near optimal coronary vasculature in the organs of adult mammals? We examine this hypothesis using a powerful and universal method, built on physical and physiological principles, for the determination of globally energetically optimal arterial trees. The method is based on simulated annealing, and can be used to examine arteries in hollow organs with arbitrary tissue geometries. We demonstrate that the approach can generate in silico vasculatures which closely match porcine anatomical data for the coronary arteries on all length scales, and that the optimized arterial trees improve systematically as computational time increases. The method presented here is general, and could in principle be used to examine the arteries of other organs. Potential applications include improvement of medical imaging analysis and the design of vascular trees for artificial organs. dataData for various parts of the paper are contained in appropriate directories, and include matlab files for plotting where appropriate.

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2016
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; NARCIS
    Dataset . 2016
    License: CC 0
    Data sources: Datacite; NARCIS
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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      ZENODO
      Dataset . 2016
      License: CC 0
      Data sources: ZENODO
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      DRYAD; NARCIS
      Dataset . 2016
      License: CC 0
      Data sources: Datacite; NARCIS
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    Authors: Scriven, Sarah A.; Beale, Colin Michael; Benedick, Suzan; Hill, Jane K.;

    Raw butterfly capture dataRaw data on the capture/recapture events of each individual butterfly marked and captured in the field during the study. See ReadMe file for description of column headings.RawButterflyCaptureData.csvR script for summary statistics and chi-squaredR script file containing code to calculate summary statistics (e.g. the number of individuals captured/recaptured/crossing the boundary etc.) and chi-squared tests presented in the study. Calculations for Figure 3 are also included.SummaryStatisticsChi2_Script.RDistances moved (n=20 species)File containing total distances (m) moved by forest and plantation individuals (individuals marked in forest and plantations, respectively) that were recaptured during the study. All species (n=20) that were recaptured in a different trap are included in the dataset. Column headings: UniqueIDF: Unique number given to every forest individual to study its movement. TotDistF: Total distance moved (m) by each forest individual that moved to a different trap. UniqueIDP: Unique number given to every plantation individual to study its movement. TotDistP: Total distance moved (m) by each plantation individual that moved to a different trap.TotalDistances20Species.csvDistances moved (n=12 species)File containing total distances (m) moved by forest and plantation individuals (individuals marked in forest and plantations, respectively) that were recaptured during the study. Only species that were recaptured in both habitats and moved to a different trap are included in the dataset (n=12 species). Column headings: UniqueIDF: Unique number given to every forest individual to study its movement. TotDistF: Total distance moved (m) by each forest individual that moved to a different trap. UniqueIDP: Unique number given to every plantation individual to study its movement. TotDistP: Total distance moved (m) by each plantation individual that moved to a different trap.TotalDistances12Species.csvR script for analysis of distances movedR script file containing code to calculate total distances moved by forest and plantation individuals and analyse differences in these distances using Mann-Whitney U tests.DistancesMoved_Script.RGLMM input variablesInput variables used in Generalized Linear Mixed Models (GLMMs) that examine whether the proportion of individuals per species crossing the habitat boundary was influenced by species' traits, abundance and habitat of first capture. See ReadMe file for description of column headings.GLMMInputVariables.csvGLMM input variables with site identityInput variables used in Generalized Linear Mixed Models (GLMMs) that examine whether the proportion of individuals per species crossing the habitat boundary was influenced by species' traits, abundance and habitat of first capture. Site identity was included as a random effect in this analysis. See ReadMe file for description of column headings.GLMMInputVariablesSite.csvR script for GLMM analysisR script file containing code to perform Generalized Linear Mixed Models (GLMMs) that examine the influence of species traits, abundance and habitat of first capture on boundary crossing. This also includes code for calculating logit probabilities and confidence intervals used in Figure 4, as well as the supplementary analysis whereby site identity was included as a random effect (Appendix S2 and Table S2).GLMMAnalysis_Script.RForest habitat measurementsData from the 13 environmental characteristics measured in forest habitats in order to assess the similarity of sample sites. See ReadMe file for description of column headings.ForestHabitatMeasurements.csvPlantation habitat measurementsData from the five environmental characteristics measured in plantation habitats in order to assess the similarity of sample sites. See ReadMe file for description of column headings.PlantationHabitatMeasurements.csv Fragmentation of natural habitats can be detrimental for species if individuals fail to cross habitat boundaries to reach new locations, thereby reducing functional connectivity. Connectivity is crucial for species shifting their ranges under climate change, making it important to understand factors that might prevent movement through human-modified landscapes. In tropical regions, rain forests are being fragmented by agricultural expansion, potentially isolating populations of highly diverse forest-dependent species. The likelihood of crossing habitat boundaries is an important determinant of species dispersal through fragmented landscapes, and so we examined movement across rain forest-oil palm plantation boundaries on Borneo by using relatively mobile nymphalid butterflies as our model study taxon. We marked 1666 individuals from 65 species, and 19 percent (100/527) of recaptured individuals crossed the boundary. Boundary crossing was relatively frequent in some species, and net movement of individuals was from forest into plantation. However, boundary crossing from forest into plantation was detected in less than 50 percent (12/28) of recaptured species and was dominated by small-sized butterfly species whose larval host plants occurred within plantations. Thus, while oil palm plantations may be relatively permeable to some species, they may act as barriers to the movement of forest-dependent species (i.e., species that require rain forest habitat to breed), highlighting the importance of maintaining forest connectivity for conserving rain forest species.

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    ZENODO
    Dataset . 2016
    License: CC 0
    Data sources: ZENODO
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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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    DRYAD; NARCIS
    Dataset . 2016
    License: CC 0
    Data sources: Datacite; NARCIS
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      ZENODO
      Dataset . 2016
      License: CC 0
      Data sources: ZENODO
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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      DRYAD; NARCIS
      Dataset . 2016
      License: CC 0
      Data sources: Datacite; NARCIS
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    Authors: Puttick, Mark N.;

    Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model. Under simulated phylogenies and data, likelihood-based models are generally accurate when estimating ancestral node values. Analyses with combined fossil and extant data always outperform analyses with extant species alone, even when around one quarter of the fossil information is incorrect. These results are especially pronounced when model assumptions are violated, such as when there is a trend away from the root value. Fossil data are of particular importance when attempting to estimate the root node character state. Attempts should be made to include fossils in analysis of discrete traits under likelihood, even if there is uncertainty in the fossil trait data. runSimulationsThis file contains R scripts to simulated discrete traits and phylogenies used in the analyses

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    DRYAD; NARCIS
    Dataset . 2016
    License: CC 0
    Data sources: Datacite; NARCIS
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    ZENODO
    Dataset . 2016
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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      DRYAD; NARCIS
      Dataset . 2016
      License: CC 0
      Data sources: Datacite; NARCIS
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      ZENODO
      Dataset . 2016
      License: CC 0
      Data sources: ZENODO
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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    Authors: Lamb, Philip D.; Hunter, Ewan; Pinnegar, John K.; Creer, Simon; +2 Authors

    Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis, and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding we conducted a structured review and meta-analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope =0.52 ±0.34, p<0.01)), albeit it with a large degree of uncertainty. None of the tested moderators: sequencing platform type, the number of species used in a trial, or the source of DNA were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilised for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study. Effect sizes, and confidence intervals for meta-analysisThis file contains all the effect sizes, confidence intervals, and grouping variables that were used in the meta-analysis.slopes_2.csv

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    DANS-EASY
    Dataset . 2018
    Data sources: B2FIND
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    ZENODO
    Dataset . 2018
    License: CC 0
    Data sources: ZENODO
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    DRYAD; NARCIS
    Dataset . 2018
    License: CC 0
    Data sources: Datacite; NARCIS
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      DANS-EASY
      Dataset . 2018
      Data sources: B2FIND
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      ZENODO
      Dataset . 2018
      License: CC 0
      Data sources: ZENODO
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      DRYAD; NARCIS
      Dataset . 2018
      License: CC 0
      Data sources: Datacite; NARCIS
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    Authors: Gonzalez-Quevedo, Catalina; Davies, Richard G.; Phillips, Karl P.; Spurgin, Lewis G.; +2 Authors

    Understanding the spatial scale at which selection acts upon adaptive genetic variation in natural populations is fundamental to our understanding of evolutionary ecology, and has important ramifications for conservation. The environmental factors to which individuals of a population are exposed can vary at fine spatial scales, potentially generating localized patterns of adaptation. Here, we compared patterns of neutral and major histocompatibility complex (MHC) variation within an island population of Berthelot's pipit (Anthus berthelotii) to assess whether landscape-level differences in pathogen-mediated selection generate fine-scale spatial structuring in these immune genes. Specifically, we tested for spatial associations between the distribution of avian malaria, and the factors previously shown to influence that distribution, and MHC variation within resident individuals. Although we found no overall genetic structure across the population for either neutral or MHC loci, we did find localized associations between environmental factors and MHC variation. One MHC class I allele (ANBE48) was directly associated with malaria infection risk, while the presence of the ANBE48 and ANBE38 alleles within individuals correlated (positively and negatively, respectively) with distance to the nearest poultry farm, an anthropogenic factor previously shown to be an important determinant of disease distribution in the study population. Our findings highlight the importance of considering small spatial scales when studying the patterns and processes involved in evolution at adaptive loci. Microsatellite genotypesMicrosats.xlsxMHC genotypes by zoneThis file contains the MHC genotypes for 310 Berthelot's pipits divided by zone. There are four zones. The first part of the table shows the frquency of each MHC allele in each of the four geographical zones.

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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    DRYAD; NARCIS
    Dataset . 2016
    License: CC 0
    Data sources: Datacite; NARCIS
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    ZENODO
    Dataset . 2016
    License: CC 0
    Data sources: ZENODO
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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      DRYAD; NARCIS
      Dataset . 2016
      License: CC 0
      Data sources: Datacite; NARCIS
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      ZENODO
      Dataset . 2016
      License: CC 0
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Smithson, Timothy R.; Browne, Michael A. E.; Davies, Sarah J.; Marshall, John E. A.; +3 Authors

    The Visean stage of the Mississippian was a time of rapid tetrapod diversification which marks the earliest appearance of temnospondyls, microsaurs and the limbless aïstopods. Tetrapod finds from this stage are very rare and only a dozen sites are known worldwide. Here we announce the discovery of a new Visean site in Fife, Scotland, of Asbian age, and from it describe a new species of the baphetoid Spathicephalus. These specimens represent the oldest known baphetoid by three million years, yet belong to the most specialized members of the clade. Unlike typical baphetoids with large marginal teeth and palatal fangs characteristic of early tetrapods, spathicephalids had very broad flattened heads with a dentition consisting of a large number of small, uniform teeth. Spathicephalids were probably one of the earliest tetrapod groups to use suction feeding on small, aquatic prey. Palynological and sedimentological analysis indicates that the new fossil bed was deposited in a large, stratified, freshwater lake that became increasingly saline. Smithson et al. A new Mississippian tetrapod Supporting InformationThe file contains a summary of the palynology of the new site. A list of species is given together with two plates of photomicrographs showing each of the spore species recovered.Smithson et al. A new Mississippian tetrapod Sup Info.docx

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    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
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    ZENODO
    Dataset . 2018
    License: CC 0
    Data sources: ZENODO
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    DRYAD; NARCIS
    Dataset . 2018
    License: CC 0
    Data sources: Datacite; NARCIS
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      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2018
      License: CC 0
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; NARCIS
      Dataset . 2018
      License: CC 0
      Data sources: Datacite; NARCIS
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1,117 Research products
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Tanner, Alastair R.; Fuchs, Dirk; Winkelmann, Inger E.; Gilbert, Thomas P.; +9 Authors

    Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian–Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates. aligned_supermatrix_36156_x_52_phylipAligned supermatrix, 180 genes, 36,156 amino acid positions, 52 taxa. Phylip format.ceph_1aug_36156

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    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Dataset . 2017
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; NARCIS
    Dataset . 2017
    License: CC 0
    Data sources: Datacite; NARCIS
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2017
      License: CC 0
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; NARCIS
      Dataset . 2017
      License: CC 0
      Data sources: Datacite; NARCIS
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Rimington, William R.; Pressel, Silvia; Duckett, Jeffrey G.; Field, Katie J.; +2 Authors

    Arbuscular mycorrhizas are widespread in land plants including liverworts, some of the closest living relatives of the first plants to colonise land 500 MYA. Previous investigations reported near-exclusive colonisation of liverworts by the most recently evolved arbuscular mycorrhizal fungi, the Glomeraceae, indicating a recent acquisition from flowering plants at odds with the widely-held notion that arbuscular mycorrhizal-like associations in liverworts represent the ancestral symbiotic condition in land plants. We performed an analysis of symbiotic fungi in 674 globally-collected liverworts using molecular phylogenetics and electron microscopy. Here we show every order of arbuscular mycorrhizal fungi colonises early-diverging liverworts, with non-Glomeraceae being at least ten times more common than in flowering plants. Arbuscular mycorrhizal fungi in liverworts and other ancient plant lineages (hornworts, lycopods and ferns) were delimited into 58 taxa and 36 singletons, of which at least 43 are novel and specific to liverworts. The discovery that early plant lineages are colonised by early-diverging fungi supports the hypothesis that arbuscular mycorrhizas are an ancestral symbiosis for all land plants. Figure_1_alignmentAlignment of Glomeromycotina fungi sequences used to produce phylogenetic tree presented in Figure 1. Sequence alignment was performed using MUSCLE algorithms within MEGA7.Figure_1_treeMaximum likelihood phylogenetic tree of Glomeromycotina fungi that can be seen in Figure 1. Tree is in Newick format, having been produced in MEGA7 using the generalised time reversible model with invariant gamma rates and 1,000 bootstrap replicates.

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    ZENODO
    Dataset . 2018
    License: CC 0
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DRYAD; NARCIS
    Dataset . 2018
    License: CC 0
    Data sources: Datacite; NARCIS
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2018
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Dataset . 2018
      License: CC 0
      Data sources: ZENODO
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      DRYAD; NARCIS
      Dataset . 2018
      License: CC 0
      Data sources: Datacite; NARCIS
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2018
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Gomez-Llano, Miguel Angel; Navarro-López, Eva Maria; Gilman, Robert Tucker;

    Sexual imprinting is the learning of a mate preference by direct observation of the phenotype of another member of the population. Sexual imprinting can be paternal, maternal, or oblique if individuals learn to prefer the phenotypes of their fathers, mothers, or other members of the population, respectively. Which phenotypes are learned can affect trait evolution and speciation rates. “Good genes” models of polygynous systems predict that females should evolve to imprint on their fathers, because paternal imprinting helps females to choose mates that will produce offspring that are both viable and sexy. Sexual imprinting by males has been observed in nature, but a theory for the evolution of sexual imprinting by males does not exist. We developed a good genes model to study the conditions under which sexual imprinting by males or by both sexes can evolve and to ask which sexual imprinting strategies maximize the fitness of the choosy sex. We found that when only males imprint, maternal imprinting is the most advantageous strategy. When both sexes imprint, it is most advantageous for both sexes to use paternal imprinting. Previous theory suggests that, in a given population, either males or females but not both will evolve choosiness in mating. We show how environmental change can lead to the evolution of sexual imprinting behavior by both sexes in the same population. Vecor_fields

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND