cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xwdbrv1b8
title: Center-of-mass and minimal speed limits of the great hammerhead

description: The great hammerhead is denser than water, and hence relies on
 hydrodynamic lift to compensate for its lack of buoyancy, and on
 hydrodynamic moment to compensate for a possible misalignment between
 centers of mass and buoyancy. Because hydrodynamic forces scale with the
 swimming speed squared, whereas buoyancy and gravity are independent of
 it, there is a critical speed below which the shark cannot generate enough
 lift to counteract gravity, and there are anterior and posterior
 center-of-mass limits beyond which the shark cannot generate enough
 pitching moment to counteract the buoyancy-gravity couple. The speed and
 center-of-mass limits were found from numerous wind-tunnel experiments on
 a scaled model of the shark. In particular, it was shown that the margin
 between the anterior and posterior center-of-mass limits is a few tenths
 of the product between the length of the shark and the ratio between its
 weight in and out of water; a diminutive 1% body length. The paper
 presents the wind tunnel experiments, and discusses the roles that the
 cephalofoil and the pectoral- and caudal- fins play in longitudinal
 balance of a shark.
description: The model of the great hammerahead was designed using
 SolidWorks®2014. Each '*stl' file is associated with a single
 part of the model. Forces on the model were measured in
 a 1m by 1m by 3m subsonic wind tunnel at 50 m/s. Each file contains forces
 amd moments measured on a particular configuration at angles of attack
 ranging between -15 to +17 degrees.    
description: All data files - these are files that end with '*cfc' -
 are ASCII.  'List of experiments' associates
 a data file with the particular configuration.
 'List of parameters' explains each column in a data
 file. All model files end with
 '*stl'.
 ' LongitudinalBalanceOfTheGreatHammerhead252Drawings.pdf' gives an overview of the model
DOI: 10.5061/dryad.sqv9s4n1m
title: Data from: Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA

description: Many cells in the thorax of Drosophila were found to stall during
 replication, a phenomenon known as underreplication. Unlike
 underreplication in nuclei of salivary and follicle cells, this stall
 occurs with less than one complete round of replication. This stall point
 allows precise estimations of early-replicating euchromatin and
 late-replicating heterochromatin regions, providing a powerful tool to
 investigate the dynamics of structural change across the genome. We
 measure underreplication in 132 species across the Drosophila genus and
 leverage this data to propose a model for estimating the rate at which
 additional DNA is accumulated as heterochromatin and euchromatin and also
 predict the minimum genome size for Drosophila. According to comparative
 phylogenetic approaches, the rates of change of heterochromatin differ
 strikingly between Drosophila subgenera. While these subgenera differ in
 karyotype, there were no differences by chromosome number, suggesting
 other structural changes may influence accumulation of heterochromatin.
 Measurements were taken for both sexes, allowing the visualization of
 genome size and heterochromatin changes for the hypothetical path of XY
 sex chromosome differentiation. Additionally, the model presented here
 estimates a minimum genome size in Sophophora remarkably close to the
 smallest insect genome measured to date, in a species over 200 million
 years diverged from Drosophila.
description: Levels of thoracic underreplication were measured using flow
 cytometry in 132 species across the Drosophila genus.  These measurements
 were used to estimated the proportion of the genome which is euchromatic
 versus heterochromatic.  These data were then used to estimate the rate of
 change of euchromatin and heterochromatin in the genus and its subgenera. 
 Additionally, a phylogeny was constructed for this group for comparative
 analyses using MrBayes.  The files here include a csv of values for all
 species of interest, which includes genome size, chromosome number,
 underreplication value, amount of replicated DNA, amount of Unreplicated
 DNA, sex differences in genome size, sex differences in replicated DNA,and
 sex differences in unreplicated DNA.  A consensus tree is uploaded which
 contains 152 species. The four tree files used to construct the consensus
 tree are also included.  A tree file which has been adjusted to
 representevolutionary time for analyses is also included.  Separate tree
 files trimmed for male and female data are also included.
description: These data include the phylogenies used for the analyses, as well
 as a csv file which includes values measured for each species.
DOI: 10.5061/dryad.x69p8czfn
title: Data from: The upper thermal tolerance for a Texas population of the hairy maggot blow fly Chrysomya rufifacies Macquart (Diptera: Calliphoridae)

description: The hairy maggot blow fly (Chrysomya rufifacies: Macquart) is an invasive
 necrophagous fly found throughout the continental United States. Chrysomya
 rufifacies is of medical/veterinary, forensic, and ecological importance
 due to its ability to cause myiasis, colonize human remains, and displace
 native Diptera. However, little is known about their upper thermal
 tolerance, which could be used to better predict their invasion potential.
 We investigated the upper thermal tolerance of C. rufifacies exposed to
 different temperatures (20 – 45°C), times (1 – 6 h), and nutrients (no
 food or water, water only, or a food-water mixture) for both sexes and two
 age ranges (young = 6-8, old = 9-11 days post pupal emergence). As
 temperature or duration increased, the probability of knockdown increased
 (0 – 100% at 20 and 45°C and from 41 – 75% at 1 and 6 h), while the
 probability of survival decreased (99 – 2% at 20 and 45°C and from 75 –
 28% at 1 and 6 h). The availability of nutrients increased thermal
 tolerance at moderate temperatures (40 and 42°C). Female flies were more
 thermally tolerant than males (probability of knockdown = 49% vs 58%;
 probability of survival = 58 % vs 46%). Thermal tolerance did not differ
 by age. These data reveal details about the upper thermal tolerance for a
 single population of C. rufifacies, and suggest that environmental and
 organismal factors ought to be considered in order to make meaningful
 predictions about the invasion potential of C. rufifacies in North
 America.
DOI: 10.5061/dryad.brv15dv6s
title: Data from: Genetic data reveal fine-scale ecological segregation between larval plethodontid salamanders in replicate contact zones

description: Contact zones present unique opportunities to investigate ecological
 divergence, reproductive barriers, and gene flow between species. The
 two-lined salamander (Eurycea bislineata) species complex is a group of
 semiaquatic plethodontid salamanders with a reticulate evolutionary
 history that reflects the reorganization of river drainage basins.
 Although evidence for widespread, ancient introgression suggests an
 absence of reproductive isolating mechanisms in the early evolutionary
 history of the group, modern contact zones reveal a broader diversity of
 outcomes—with some putative species pairs occurring in sympatry and others
 exhibiting narrow hybrid zones. Here, we used RADcap data to investigate
 gene flow and ecological divergence in replicate contact zones between two
 species in the Appalachian foothills. Our results demonstrate that gene
 flow between these species is absent or rare, and larvae show strong,
 fine-scale ecological segregation among riffles, runs, and pools in
 streams. These results reinforce the more ambiguous conclusions of
 previous studies that suggested the evolutionary distinctiveness of these
 two species and underscore the importance of ecological factors in shaping
 local distributions.
DOI: 10.5061/dryad.76hdr7stb
title: Data for: A size principle for recruitment of Drosophila leg motor neurons

description: To move the body, the brain must precisely coordinate patterns of activity
 among diverse populations of motor neurons. In many species, including
 vertebrates, the motor neurons innervating a given muscle fire in a
 specific order that is determined by a gradient of cellular size and
 electrical excitability. This hierarchy allows premotor circuits to
 recruit motor neurons of increasing force capacity in a task-dependent
 manner. However, it remains unclear whether such a size principle also
 applies to species with more compact motor systems, such as the fruit
 fly, Drosophila melanogaster, which has just 53 motor neurons per
 leg. Using in vivo calcium imaging and
 electrophysiology, we found that genetically-identified motor neurons
 controlling flexion of the fly tibia exhibit a gradient of anatomical,
 physiological, and functional properties consistent with the size
 principle. Large, fast motor neurons control high force, ballistic
 movements while small, slow motor neurons control low force, postural
 movements. Intermediate neurons fall between these two extremes. In
 behaving flies, motor neurons are recruited in order from slow to fast.
 This hierarchical organization suggests that slow and fast motor neurons
 control distinct motor regimes. Indeed, we find that optogenetic
 manipulation of each motor neuron type has distinct effects on the
 behavior of walking flies.
description: This dataset contains preprocessed records for 1)
 electrophysiology recordings with membrane voltage or EMG current,
 stimulus parameters, exposure times from synchronous video recordings, as
 well as the position of a force probe calculated from simultaneous videos,
 2) limb positions tracked from video recordings during optogenetic
 perturbation, and 3) recordings of the position and velocity of a ball
 during optogenetic perturbation in flies walking on the ball.
description: Please see README file for instructions.
DOI: 10.5061/dryad.2v6wwpzjj
title: Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

description: Landscape genomics studies focus on identifying candidate genes under
 selection via spatial variation in abiotic environmental variables, but
 rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus
 harrisii) is found only on the environmentally heterogeneous island of
 Tasmania and is threatened with extinction by a nearly 100% fatal,
 transmissible cancer, devil facial tumor disease (DFTD). Devils persist in
 regions of long-term infection despite epidemiological model predictions
 of species’ extinction, suggesting possible adaptation to DFTD. Here, we
 test the extent to which spatial variation and genetic diversity are
 associated with the abiotic environment and/or DFTD. We employ
 genetic-environment association analyses using a RAD-capture panel
 including 6,886 SNPs from 3,286 individuals sampled pre- and post-disease
 arrival. Pre-disease, we find significant correlations of allele
 frequencies with environmental variables, including 365 unique loci linked
 to 71 genes, suggesting local adaptation to abiotic environment. The
 majority of candidate loci detected pre-DFTD were not detected post
 disease arrival. Several post-DFTD candidate loci were associated with
 disease prevalence and were in linkage disequilibrium with genes involved
 in tumor suppression and immune response. Loss of apparent signal of
 abiotic local adaptation post-disease suggests swamping by the strong
 selection resulting from the rapid onset of DFTD.
description: CSV file containing sample information for devils sampled
 pre-DFTD arrival Pre_Devils.csv
 CSV file containing sample information for devils sampled
 post-DFTD arrival Post_Devils.csv
 Filtered VCF file containing individuals sampled pre-DFTD
 arrival pre_vcf.vcf.gz Filtered
 VCF file containing individuals sampled post-DFTD arrival
 post_vcf.vcf.gz
DOI: 10.5061/dryad.gb5mkkwmh
title: Data from: Ambiguous species boundaries: hybridization and morphological variation in two closely related Rubus species along altitudinal gradients

description: Although hybridization frequently occurs among plant species, hybrid zones
 of divergent lineages formed at species boundaries are less common and may
 not be apparent in later generations of hybrids with more parental-like
 phenotypes, as a consequence of backcrossing. To determine the effects of
 dispersal and selection on species boundaries, we compared clines in leaf
 traits and molecular hybrid index along two hybrid zones on Yakushima
 Island, Japan, in which a temperate (Rubus palmatus) and subtropical
 (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in
 the two hybrid zones had narrower clines at 600 m a.s.l. than the
 molecular hybrid index and common garden tests confirmed that some leaf
 traits, including leaf sinus depth that is a major trait used in species
 identification, are genetically divergent between these closely related
 species. The sharp transition in leaf phenotypic traits compared to
 molecular markers indicated divergent selection pressure on the hybrid
 zone structure. We suggest that species boundaries based on neutral
 molecular data may differ from those based on observed morphological
 traits.
DOI: 10.5061/dryad.sbcc2fr3k
title: Data from: Equivocal evidence for a change in balance between selfing and pollinator-mediated reproduction in annual Brassicaceae growing along a rainfall gradient

description: Because many plants ensure their reproductive success using some level of
 self-fertilization, it is predicted that the balance between
 pollinator-mediated pollen transfer and autonomous selfing will be
 correlated with habitat harshness and pollinator activity. To study these
 correlations, we used three annual species that differ in their
 self-incompatibility and compared their reproductive success in the form
 of fruit production and seed viability, with and without pollinators,
 along a rainfall gradient and in relation to pollinator activity. We found
 that pollinator activity decreased with increasing aridity. However,
 although the reproductive success in the absence of pollinators fitted the
 species’ level of self-incompatibility, no clear trend was detected
 between pollinator visits or site harshness and relative reproductive
 success. Only one of the species, Sinapis alba, showed a consistent
 increase in autonomous selfing with both increased aridity and decreased
 pollinator visits, a finding that was supported by an increase in the
 viability of seeds produced in the absence of pollinators. Nevertheless,
 unlike our prediction, the absolute number of seeds produced per S. alba
 flower increased with aridity. Our overall findings suggest that despite
 decreasing pollinator abundance and diversity with increasing aridity,
 reproductive success of annual species, even of those with high
 self-incompatibility, remains relatively high. While there may be several
 mechanisms governing these results, the overall constant seed production
 despite environmental uncertainties may be part of the mechanism by which
 plants in arid ecosystems buffer environmental variations.
description: Fruit & seed data - JSE-2020-05-118
 All  methods are described in the paper:
 "Equivocal evidence for a change in balance between
 selfing and pollinator-mediated reproduction in annual Brassicaceae
 growing along a rainfall gradient"
description: Missing values are presented with the entry "NA"
DOI: 10.5061/dryad.f7m0cfxsd
title: Data from: A phylogenetic- and trait-based analysis of community assembly in a subtropical forest in central China

description: Despite several decades of study in community ecology, the relative
 importance of the ecological processes that determine species
 co-occurrence across spatial scales remains uncertain. Some of this
 uncertainty may be reduced by studying the scale dependency of community
 assembly in the light of environmental variation. Phylogenetic and
 functional trait information are often used to provide potentially
 valuable insights into the drivers of community assembly. Here, we
 combined phylogenetic- and trait-based tests to gain insights into
 community processes at four spatial scales in a large stem-mapped
 subtropical forest dynamics plot in central China. We found that all of
 the six leaf economic traits measured in this study had weak, but
 significant, phylogenetic signal. Non-random phylogenetic and trait-based
 patterns associated with topographic variables indicate that deterministic
 processes tend to dominate community assembly in this plot. Specifically,
 we found that, on average, co-occurring species were more phylogenetically
 and functionally similar than expected throughout the plot at most spatial
 scales and assemblages of less similar than expected species could only be
 found on finer spatial scales. In sum, our results suggest that the
 trait-based effects on community assembly change with spatial scale in a
 predictable manner and the association of these patterns with topographic
 variables, indicates the importance of deterministic processes in
 community assembly relatively to random processes.
description: This dataset includes one Excel files, a list of trait data used
 in this study, species with latin name and individuals (please see
 <strong>Materials and methods</strong><em><strong>
 </strong></em>for details).
description: The definitions for all columns (i.e. variables) within each
 sheet have been listed in the meta sheet.
DOI: 10.5061/dryad.qz612jmbs
title: Data from: Drought legacies are short, prevail in dry conifer forests and depend on growth variability.

description: The negative impacts of drought on forest growth and productivity last for
 several years generating legacies, although the factors that determine why
 such legacies vary across sites and tree species remain unclear. We used
 an extensive network of tree-ring width (RWI, ring-width index) records of
 16 tree species from 567 forests, and high-resolution climate and NDVI
 datasets across Spain during the common period 1982‒2008 to test the
 hypothesis that climate conditions and growth features modulate legacy
 effects of drought on forests. Legacy effects of drought were calculated
 as the differences between detrended-only RWI and NDVI series (i.e. after
 removing long-term growth trends) and pre-whitened RWI and NDVI series
 predicted by a model including drought intensity. Superposed epoch
 analysis (SEA) was used to estimate whether legacy effects differed from
 random. Finally, legacy effects were related to water balance, growth
 persistence and variability, and tree species identity. We found a
 widespread occurrence of drought legacy effects in both RWI and NDVI, but
 they were seldom significant. According to SEA, first-year drought
 legacies were negative and different from random in 9% and 5% of the RWI
 and NDVI series, respectively. The number of significant second- and
 third-year legacies was substantially lower. Differences between RWI and
 NDVI legacies indicate that canopy greenness and radial-growth responses
 to drought are decoupled. We found variations in legacies between tree
 species with gymnosperms presenting larger first-year drought legacies
 than angiosperms, which were exposed to less severe droughts. Greater
 growth variability can explain the presence of first-year RWI legacies in
 gymnosperms from dry sites despite the relationship between growth
 variability and legacies was complex. “Synthesis” Accounting for species
 and site responses to drought provides a better understanding of the
 magnitude and duration of drought legacies on forest growth and
 productivity. Despite the widespread occurrence of growth reductions in
 the years during and after drought occurrence, significant legacies were
 not very common, mostly lasted one year and were more widespread in
 gymnosperms. These are relevant factors to be considered in the future
 when studying the consequences of drought on forest productivity and tree
 growth.
description: The dataset used in this study is part of a database of tree-ring
 width measures for tree species across their Spanish distribution. This
 dataset includes legacies of drought in growth (RWI) and NDVI in 508
 forests of 16 tree species (9 gymnosperms and 7 angiosperms) and related
 variables.
DOI: 10.5061/dryad.4xgxd2568
title: Code for individual-based simulations in "Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios"

description: Substantial environmental change can force a population onto a path
 towards extinction, but under some conditions, adaptation by natural
 selection can rescue the population and allow it to persist. This process,
 known as evolutionary rescue, is believed to be less likely to occur with
 greater magnitudes of random environmental fluctuations because
 environmental variation decreases expected population size, increases
 variance in population size, and increases evolutionary lag. However,
 previous studies of evolutionary rescue in fluctuating environments have
 only considered scenarios in which evolutionary rescue was likely to
 occur. We extend these studies to assess how baseline extinction risk
 (which we manipulated via changes in the initial population size, degree
 of environmental change, or mutation rate) influences the effects of
 environmental variation on evolutionary rescue following an abrupt
 environmental change. Using a combination of analytical models and
 stochastic simulations, we show that autocorrelated environmental
 variation hinders evolutionary rescue in low-extinction-risk scenarios but
 facilitates rescue in high-risk scenarios. In these high-risk cases, the
 chance of a run of good years counteracts the otherwise negative effects
 of environmental variation on evolutionary demography. These findings can
 inform the development of effective conservation practices that consider
 evolutionary responses to abrupt environmental changes.
description: A full descripition of the methods can be found in the appendix
 of the assossicated manuscript.
description: This .zip file contains the code and documentation for two
 individual-based models that simulate evolutionary rescue following an
 abrupt environmental change with different degrees of environmental
 variation. Both models assume that fitness is determined by a single
 quantitative trait. The first model incorporates environmental variation
 into the optimal phenotype (Var_theta.Cpp) and the second incorporates it
 into fecundity (Var_F.Cpp). Both models are written in C++. Documentation
 on how to run the code is given in the "README" file. 
 For detailed instructions for how to run simulations using this
 code, please see the README file. We have also provided example input
 files which will allow the user to replicate data in the manuscript.
 Information on how to use these files is also provided in the README
 file.