cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pg4f4qrk0
title: Single cell transcriptomics of of Abedinium reveals a new early-branching dinoflagellate lineage

description: Dinoflagellates possess many unique cellular characteristics with
 unresolved evolutionary histories including nuclei with greatly expanded
 genomes and chromatin packaged using histone-like proteins and
 dinoflagellate-viral nucleoproteins instead of histones, highly reduced
 mitochondrial genomes with extensive RNA editing, a mix of photosynthetic
 and cryptic secondary plastids, and tertiary plastids. Resolving the
 evolutionary origin of these traits requires understanding their ancestral
 states and early intermediates. Several deep-branching dinoflagellate
 lineages are good candidates for such reconstruction, however they tend to
 be delicate and environmentally sparse, so such analyses are not always
 simple. Here, we employ transcriptome sequencing from manually-isolated
 and microscopically documented cells to resolve the placement of two cells
 of one such genus, Abedinium, collected by ROV in deep waters off the
 coast of Monterey Bay. One cell corresponds to the only described species,
 A. dasypus, while the second cell is distinct and formally described as
 Abedinium folium, sp. nov. Abedinium has classically been assigned to the
 deep-branching dinoflagellates subgroup Noctilucea, which is weakly
 supported by phylogenetic analyses of the single characterized gene from
 any member of the genus, small subunit ribosomal RNA (SSU rRNA). However,
 a phylogenetic analysis based on 221 proteins from the transcriptome
 places Abedinium in a distinct lineage, separate from and basal to the
 Noctilucea and the rest of the core dinoflagellates. The transcriptome
 also contains evidence of a cryptic plastid functioning in the
 biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a
 mitochondrial genome with all three expected protein-coding genes (cob,
 cox1, and cox3), and the presence of some but not all
 dinoflagellate-specific chromatin packaging proteins.
DOI: 10.5061/dryad.6q573n5vz
title: The evolution of autotomy in leaf-footed bugs

description: Sacrificing body parts is one of many behaviors that animals use to escape
 predation. This trait, termed autotomy, is classically associated with
 lizards. However, several other taxa also autotomize, and this trait has
 independently evolved multiple times throughout Animalia. Despite having
 multiple origins and being an iconic anti-predatory trait, much remains
 unknown about the evolution of autotomy. Here, we combine morphological,
 behavioral, and genomic data to investigate the evolution of autotomy
 within leaf-footed bugs and allies (Insecta: Hemiptera: Coreidae +
 Alydidae). We found that the ancestor of leaf-footed bugs autotomized and
 did so slowly; rapid autotomy (&lt; 2 min) then arose multiple times.
 The ancestor likely used slow autotomy to reduce the cost of injury or to
 escape non-predatory entrapment but could not use autotomy to escape
 predation. This result suggests that autotomy to escape predation is a
 co-opted benefit (i.e., exaptation), revealing one way that sacrificing a
 limb to escape predation may arise. In addition to identifying the origins
 of rapid autotomy, we also show that across species variation in the rates
 of autotomy can be explained by body size, distance from the equator, and
 enlargement of the autotomizable appendage.
description: See read me file.
DOI: 10.15468/dl.aads99
title: Occurrence Download

description: A dataset containing 2133483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((104 2,103 2,103 1,104 1,104 2))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2133483 records from 396 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002199-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f4qrfj6sp
title: Interspecific competition slows range expansion and shapes range boundaries

description: Species expanding into new habitats as a result of climate change or human
 introductions will frequently encounter resident competitors. Theoretical
 models suggest that such interspecific competition can alter the speed of
 expansion and the shape of expanding range boundaries. However,
 competitive interactions are rarely considered when forecasting the
 success or speed of expansion, in part because there has been no direct
 experimental evidence that competition affects either expansion speed or
 boundary shape. Here we demonstrate that interspecific competition alters
 both expansion speed and range boundary shape. Using a two-species
 experimental system of the flour beetles Tribolium castaneum and Tribolium
 confusum, we show that interspecific competition dramatically slows
 expansion across a landscape over multiple generations. Using a
 parameterized stochastic model of expansion, we find that this slowdown
 can persist over the long-term. We also find that the shape of the moving
 range boundary changes continuously over many generations of expansion,
 first steepening and then becoming shallower, due to the competitive
 effect of the resident and density-dependent dispersal of the invader.
 This dynamic boundary shape suggests that current forecasting approaches
 assuming a constant shape could be misleading. More broadly, our results
 demonstrate that interactions between competing species can play a large
 role during range expansions and thus should be included in models and
 studies that monitor, forecast, or manage expansions in natural systems.
description: This ZIP archive contains R scripts and data files necessary for
 reproducing the analysis and figures of the paper. See the README file in
 the archive for further details.
DOI: 10.5061/dryad.ns1rn8ppd
title: Cancer cells optimize elasticity for efficient migration

description: Cancer progression is associated with alternations in the cytoskeletal
 architecture of cells and, consequently, their mechanical properties such
 as stiffness. Changing the mechanics of cells enables cancer cells to
 migrate and invade to distant organ sites. This process, metastasis, is
 the main reason for cancer-related mortality. Cell migration is an
 essential step toward increasing the invasive potential of cells. Although
 many studies have shown that the migratory speed and the invasion of cells
 can be inversely correlated to the stiffness of cells, some other
 investigations indicate exactly opposing results. In the current work,
 based on the strain energy stored in cells due to the contractile forces,
 we defined an energy-dependent term, migratory index, to approximate how
 changes in the mechanical properties of cells influence cell migration
 required for cancer progression. Cell migration involves both cell
 deformation and force transmission within cells. The effects of these two
 parameters can be represented equally by the migratory index. Our
 mechanical modeling and computational study show that cells depending on
 their shape, size, and other physical parameters, have a maximum migratory
 index taking place at a specific range of cell bulk stiffness, indicating
 the most favorable conditions for invasive mobility. This approximate
 model can be used to explain why the stiffness of cells varies during
 cancer progression.  We believe that the stiffness of invasive
 cells depending on the stiffness of their non-invasive counterparts is
 either decreased or increased to reach the critical condition in which the
 mobility potential of cells is approximated to be maximum.
description: Data were extracted from COMSOL Multiphysics (Solid mechanics
 Module/Hyperelastic materials)   
description: You can find extracted data from
 "Parameters_on_Migratory_Index". To repeat the simulation, refer
 to "simulation_setting" to see the set parameters to run the
 simulation. The 2D model can be found from
 "Cell_CAD_Model".
DOI: 10.5061/dryad.6wwpzgmv5
title: Data from: The evolution of competitive ability for essential resources

description: Competition for limiting resources is among the most fundamental
 ecological interactions and has long been considered a key driver of
 species coexistence and biodiversity. Species' minimum resource
 requirements, their R*s, are key traits that link individual physiological
 demands to the outcome of competition. However, a major question remains
 unanswered - to what extent are species’ competitive traits able to evolve
 in response to resource limitation? To address this knowledge gap, we
 performed an evolution experiment in which we exposed Chlamydomonas
 reinhardtii for approximately 285 generations to seven environments in
 chemostats which differed in resource supply ratios (including nitrogen,
 phosphorus and light limitation) and salt stress. We then grew the
 ancestors and descendants in common garden and quantified their
 competitive abilities for essential resources. We investigated constraints
 on trait evolution by testing whether changes in resource requirements for
 different resources were correlated. Competitive abilities for phosphorus
 improved in all populations, while competitive abilities for nitrogen and
 light increased in some populations and decreased in others. In contrast
 to the common assumption that there are trade-offs between competitive
 abilities for different resources, we found that improvements in
 competitive ability for a resource came at no detectable cost. Instead,
 improvements in competitive ability for multiple resources were either
 positively correlated or not significantly correlated. Using resource
 competition theory, we then demonstrated that rapid adaptation in
 competitive traits altered the predicted outcomes of competition. These
 results highlight the need to incorporate contemporary evolutionary change
 into predictions of competitive community dynamics over environmental
 gradients.
description: See associated paper, Phil. Trans. R. Soc. B 375: 20190247. http://dx.doi.org/10.1098/rstb.2019.0247. Relative fluorescence data were collected from populations of Chlamydomonas rheinhardtii growing in light and temperature controlled incubators, using a BioTek plate reader and imager.
DOI: 10.5061/dryad.2z34tmphj
title: Genetic drift does not sufficiently explain patterns of electric signal variation among populations of the mormyrid electric fish Paramormyrops kingsleyae

description: Communication signals serve crucial survival and reproductive functions.
 In Gabon, the widely distributed mormyrid fish Paramormyrops kingsleyae
 emits an electric organ discharge (EOD) signal with a dual role in
 communication and electrolocation that exhibits remarkable variation:
 populations of P. kingsleyae have either biphasic or triphasic EODs, a
 feature which characterizes interspecific signal diversity among the
 Paramormyrops genus. We quantified variation in EODs of 327 P. kingsleyae
 from 9 populations and compared it to genetic variation estimated from
 microsatellite loci. We found no correlation between electric signal and
 genetic distances, suggesting that EOD divergence cannot be explained by
 drift alone. An alternative hypothesis is that EOD differences are used
 for mate discrimination, which would require P. kingsleyae be capable of
 differentiating between divergent EOD waveforms. Using a
 habituation-dishabituation assay, we found that P. kingsleyae can
 discriminate between biphasic and triphasic EOD types. Nonetheless,
 patterns of genetic and electric organ morphology divergence provide
 evidence for hybridization between these signal types. Although
 reproductive isolation with respect to signal type is incomplete, our
 results suggest that EOD variation in P. kingsleaye could be a cue for
 assortative mating.
description: This dataset contains: Response data for behavioral dishabituation paradigms conducted in the field and laboratory (Behavior Directory) Raw fragement sizes and microsatellite bins (Genotyping) Output tables for EOD landmarks, and MDS scaling results (EOD_Analysis) Tables of observed penetration counts for histological analysis (Histology) The README.md files in the subfolders describe the data in more detail.  See Picq et al. (2020) Genetic drift does not sufficiently explain patterns of electric signal variation among populations of the mormyrid electric fish <i>Paramormyrops kingsleyae </i>for a full description of methods utilized.  
description: This repositiory includes instructions raw data, or instructions
 for obtaining, all data utilized in Picq et al.
 (2020) Genetic drift does not sufficiently explain patterns of electric signal variation among populations of the mormyrid electric fish <i>Paramormyrops kingsleyae.</i> A companion repositiory for all code for data analysis is located at: http://github.com/msuefishlab/picq_etal_genetic_drift_2020
DOI: 10.5061/dryad.n2z34tmsx
title: Egg-induced changes to sperm phenotypes shape patterns of multivariate selection on ejaculates

description: Ejaculates exhibit extraordinary phenotypic diversity and rapid rates of
 evolution, yet the adaptive value of most sperm traits remains equivocal.
 Recent findings suggest that to understand how selection targets
 ejaculates we must recognize that female-imposed physiological conditions
 often alter ejaculate phenotypes. These phenotypic changes to ejaculates
 may influence the relationships among sperm traits and their association
 with fitness. Here, we show that chemical substances released by eggs
 (known to modify sperm physiology and behavior) alter patterns of
 selection on a suite of sperm traits in the mussel Mytilus
 galloprovincialis. We use multivariate selection analyses to characterize
 linear and nonlinear selection acting on sperm traits in (a) seawater
 alone, and (b) seawater containing egg-derived chemicals (egg water). Our
 analyses revealed that nonlinear selection on canonical axes of multiple
 traits (notably sperm velocity, sperm linearity and percentage of motile
 sperm) was the most important form of selection overall, but importantly
 these patterns were only evident when sperm phenotypes were measured in
 egg water. These findings reveal the subtle way that females can alter
 patterns of selection, with the implication that overlooking
 environmentally-moderated changes to ejaculate phenotypes may result in
 erroneous interpretations of how selection targets phenotypic
 (co)variation in ejaculate traits.
description: <strong>File: MSDATA.EW.FSW_17</strong>
 BLOCK = block number; ID = male ID within block; male.ID =
 individual male ID; MOTILECOUNT* = number of motile sperm tracked; ALH*
 = amplitude of lateral head movement; BCF* = beat-cross frequency; LIN*
 = linearity; STR* = straightness; VAP* = average-path velocity; VCL*
 = curvilinear velocity; VSL* = straight-line velocity; PERCENTTOTAL*
 = percentage of motile sperm in sample; PROPORTION = proportion of eggs
 fertilised (out of 200); RELATIVE = relative fertilisation
 success *If a trait has an 'e' at the end, it
 was measured in egg water, if 'f', then taken in filtered
 seawater <strong>File:
 MSEXP_Morphology_17</strong> male.ID = individual
 male ID; BLOCK = block number; Head.Length = sperm head length;
 Tail.Length = sperm flagellum length; Total.Length = Total sperm
 length
DOI: 10.5061/dryad.tx95x69tc
title: Tracking long-distance migration of marine fishes using compound-specific stable isotope analysis of amino acids

description: The long-distance migrations by marine fishes are difficult to track by
 field observation. Here, we propose a new method to track such migrations
 using stable nitrogen isotopic composition at the base of the food web
 (δ15NBase), which allows for direct comparison of isotope ratios between
 proxy organisms of the isoscape and the target migratory animal. We
 initially constructed a δ15NBase isoscape in the North Pacific by bulk and
 compound-specific isotope analyses of copepods (n = 360 and 24,
 respectively). We then determined retrospective δ15NBase values of
 spawning chum salmon (Oncorhynchus keta) from their vertebral centra (10
 sections from each of two salmon), and estimated their migration routes by
 using a state-space model. Our isotope tracking method successfully
 reproduced a known chum salmon migration route between the Okhotsk and
 Bering seas, and our findings suggest the presence of a migration route to
 the Bering Sea Shelf during a later growth stage.
DOI: 10.5061/dryad.vmcvdncpw
title: Ecological rigidity and the hardness of selection in the wild

description: Hutchinson’s ecological theater and evolutionary play is a classical view
 of evolutionary ecology—ecology provides a template in which evolution
 occurs. An opposing view is that ecological and evolutionary changes are
 like two actors on a stage, intertwined by density- and
 frequency-dependence. These opposing views correspond to hard and soft
 selection respectively. While often presented as diametrically opposed,
 both types of selection can occur simultaneously, yet we largely lack
 knowledge of the relative importance of hard versus soft selection in the
 wild. I use a dataset of 3000 individual gall makers from 15 wild local
 populations over 5 years to investigate the hardness of selection. I show
 that enemy attack consistently favors some gall sizes over others (hard
 selection) but that these biases can be fine-tuned by density- and
 frequency-dependence (soft selection). As a result, selection is hard and
 soft in roughly equal measures, but the importance of each type varies as
 species interactions shift. I conclude that eco-evolutionary dynamics
 should occur when a mix of hard and soft selection acts on a population.
 This work contributes to the rapprochement of disparate views of
 evolutionary ecology—ecology is neither a rigid theater nor a flexible
 actor, but instead embodies components of both.
DOI: 10.5061/dryad.gxd2547h3
title: Scavenger community structure along an environmental gradient from boreal forest to alpine tundra in Scandinavia

description: Scavengers can have strong impacts on food webs, and awareness of their
 role in ecosystems have increased during the last decades. In our study,
 we used baited camera traps to quantify the structure of the winter
 scavenger community in central Scandinavia across a forest-alpine
 continuum and assess how climatic conditions affected spatial patterns of
 species occurrences. Canonical correspondence analysis revealed that the
 main habitat type (forest or alpine tundra) and snow depth were main
 determinants of community structure. According to hierarchical modelling
 of the species community, species richness was higher in forest than in
 alpine habitat but was only weakly associated with temperature and snow
 depth. However, we observed stronger and more diverse impacts of these
 covariates on individual species. Occurrence at baits of habitat
 generalists (red fox, golden eagle and common raven) typically increased
 at low temperatures and high snow depth, probably due to increased
 energetic demands and lower live prey availability in harsh winter
 conditions. On the contrary, occurrence of forest specialists (e.g.
 Eurasian jay) tended to decrease in deep snow, which is possibly a
 consequence of reduced bait detectability and accessibility. In general,
 the influence of environmental covariates on species richness and
 occurrence was lower in alpine tundra than in forests, and habitat
 generalists dominated the scavenger communities in both habitat types.
 Following forecasted climate change, altered environmental conditions is
 likely to cause range expansion of boreal species and range contraction of
 typical alpine species such as the arctic fox. Our results suggest that
 altered snow conditions will be a main driver of change.
description: Data was collected with baited camera traps and processed with
 excel.
DOI: 10.15468/dl.cje898
title: Occurrence Download

description: A dataset containing 442 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aeschynomene evenia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 442 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002235-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9cnp5hqf4
title: Data from: Long-term mark-recapture and growth data for large-sized migratory brown trout (Salmo trutta) from Lake Mjøsa, Norway

description: This data package contains two unique publicly available time series of
 individual-based data originating from a 51-year mark-recapture study of a
 land-locked population of large-sized migratory brown trout (Salmo trutta)
 in Norway: the Hunder trout. In the period 1966-2015, nearly 14,000 adult
 Hunder trout have been captured and individually marked during their
 spawning migration from Lake Mjøsa to the river Gubrandsdalslågen. Almost
 a third of those individuals were later recaptured alive during a later
 spawning run and/or captured by fishermen and reported dead or alive. This
 has resulted in the first data series: a mark-recapture-recovery
 dataset spanning half a century and more than 18,000 capture records. The
 second data series consists of additional data on juvenile and adult
 growth and life-history schedules from half of the marked individuals,
 obtained by means of scale sample analysis. The two datasets offer a rare
 long-term perspective on individuals and population dynamics and provide
 unique opportunities to gain insights into questions surrounding
 management, conservation, and restoration of migratory salmonid
 populations and freshwater ecosystems.  
description: Data collection is documented in detail in the accompanying data
 paper: Moe SJ, Nater CR, Rustadbakken A,
 Vøllestad LA, Lund E, Qvenild T, Hegge O, Aass P (2020) Long-term
 mark-recapture and growth data for large-sized migratory brown trout
 (<i>Salmo trutta</i>) from Lake Mjøsa, Norway. Biodiversity
 Data Journal 8: e52157. https://doi.org/10.3897/BDJ.8.e52157
description: Detailed description of the data themselves (including metadata)
 as well as the study system and monitoring programme are provided in the
 accompanying data paper: Moe SJ, Nater CR, Rustadbakken A,
 Vøllestad LA, Lund E, Qvenild T, Hegge O, Aass P (2020) Long-term
 mark-recapture and growth data for large-sized migratory brown trout
 (<i>Salmo trutta</i>) from Lake Mjøsa, Norway. Biodiversity
 Data Journal 8: e52157. https://doi.org/10.3897/BDJ.8.e52157   It is highly recommended to thoroughly read the data paper before using the data. Users of the data files should cite both the data package and the associated data paper. We further encourage parties interested in re-using the data to contact the the data package/paper authors CRN, SJM, AR or LAV for a discussion of research ideas and potential opportunities for collaboration.