cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfjb3
title: Computational exploration of treadmilling and protrusion growth observed in fire ant rafts

description: Condensed active matter systems regularly achieve cooperative emergent
 functions that individual constituents could not accomplish alone. The
 rafts of fire ants (Solenopsis invicta) are often studied in this context
 for their ability to create structures comprised entirely of their own
 bodies, including tether-like protrusions that facilitate exploration of
 flooded environments. While similar protrusions are observed in
 cytoskeletons and cellular aggregates, they are generally dependent on
 morphogens or external gradients leaving the isolated role of local
 interactions poorly understood. Here we demonstrate through an
 ant-inspired, agent-based numerical model how protrusions in ant rafts may
 emerge spontaneously due to local interactions and how phases of
 exploratory protrusion growth may be induced by increased ant activity.
 These results provide an example in which functional morphogenesis of
 condensed active matter may emerge purely from locally-driven collective
 motion and may provide a source of inspiration for the development of
 autonomous active matter and swarm robotics.
description: The agent-based model used to generate numerical results in this
 publication was written and processed in MathWorks® MATLAB
 R2019b. Additional raw data produced from the code and
 the post-processing methods used to generate specific results presented in
 figures are provided in zip folders with the designated names of said
 figures in their titles.  Descriptions and instructions are generally
 provided in the "Run... .m" scripts provided in each
 folder.
description: A ReadMe file is available with instructions for running the
 code, and subsequently post-processing the output data.
 The code provided represents the base-level code used in
 parameters sweeps for the final results presented. Various modifications
 were made to this code in order to implement aspects such as periodic
 boundary conditions, modulated surface agent activity level, etc. in
 investigation of specific things (e.g., unconfined self-propelled particle
 trajectory behavior,  or activity's influence on global raft shape,
 respectively). Codes containing these specialty modifications are
 available in zip folders, also provided.
DOI: 10.5061/dryad.pg4f4qrnd
title: Interspecific introgression reveals a role of male genital morphology during the evolution of reproductive isolation in Drosophila

description: Rapid divergence in genital structures among nascent species has been
 posited to be an early-evolving cause of reproductive isolation, although
 evidence supporting this idea as a widespread phenomenon remains mixed.
 Using a collection of interspecific introgression lines between two
 Drosophila species that diverged ~240,000 years ago, we tested the
 hypothesis that even modest divergence in genital morphology can result in
 substantial fitness losses. We studied the reproductive consequences of
 variation in the male epandrial posterior lobes between Drosophila
 mauritiana and D. sechellia and found that divergence in posterior lobe
 morphology has significant fitness costs on several pre-fertilization and
 post-copulatory reproductive measures. Males with divergent posterior lobe
 morphology also significantly reduced the life span of their mates.
 Interestingly, one of the consequences of genital divergence was decreased
 oviposition and fertilization, which suggests that a sensory bias for
 posterior lobe morphology could exist in females, and thus posterior lobe
 morphology may be the target of cryptic female choice in these species.
 Our results provide evidence that divergence in genitalia can in fact give
 rise to substantial reproductive isolation early during species
 divergence, and they also reveal novel reproductive functions of the
 external male genitalia in Drosophila.
DOI: 10.5061/dryad.2ngf1vhms
title: Traits explain sorting of C4 grasses along a global precipitation gradient

description: Species distributions are closely associated with moisture availability,
 but the underlying mechanisms remain unresolved. Drought relations are
 especially important for plants such as C4 grasses that dominate
 seasonally dry ecosystems. Here, we test the hypothesis that C4 grass
 species sampled across global precipitation gradients show variation in
 survival under drought that can be explained by their traits. Our
 experiment subjected 18 C4 grass species to a lethal drought under
 controlled environmental conditions. The number of days until death was
 measured, along with root traits, senescence and aspects of hydraulic
 function. We identified two strategies; Drought avoiding species
 that stayed green as the water potential declined, and drought tolerating
 species that senesced more quickly but could extend survival via drought
 tolerant meristems. Plants that stay-green for longer occupied
 drier habitats and had the longest survival under drought, facilitated by
 narrow root diameter and isohydric stomatal behaviour. Plants that
 senesced quickly had thicker roots, an anisohydric strategy, and occupied
 wetter habitats. Global distributions of C4 grasses can be
 predicted by variation in rates of senescence, meristem survival, root
 traits and stomatal strategy, showing the value of these traits for
 understanding plant distributions in relation to climate.
description: The data was collected through a controlled environment
 experiment. Values presented are species means.
DOI: 10.25349/d9p89x
title: Supporting information for: Comprehensive high‐precision relocation of seismicity on the Island of Hawai‘i 1986–2018: seismicity animations

description: Abundant seismicity beneath the the Island of Hawai‘i from mantle depths
 to the surface plays a central role in understanding how volcanoes work,
 grow, and evolve at this intraplate oceanic hotspot. We perform systematic
 waveform cross‐correlation, cluster analysis, and relative relocation of
 347,445 events representing 32 years of seismicity on and around the
 island from 1986 to 2018. We successfully relocate 275,009 (79%) events
 using ∼1.7 billion differential times (P aicnd S) from ∼128 million
 similar‐event pairs. The results reveal a dramatic sharpening of
 seismicity along faults, streaks, rings, rift zones, magma pathways, and
 mantle fault zones; seismicity delineating crustal detachments on the
 flanks of Kīlauea and Mauna Loa is particularly well‐resolved. The
 resulting high‐precision spatio‐temporal image of seismicity captures
 almost the entire 1983–2018 Pu‘u ‘Ō‘ō‐Kūpaianaha eruption of Kīlauea with
 its numerous distinct episodes and wide‐ranging activity, culminating in
 the 2018 lower East Rift Zone eruption and summit collapse.
DOI: 10.5061/dryad.z8w9ghxb6
title: Cascading effects of algal warming in a freshwater community

description: 1. Much of our research on the effects of ongoing climate warming on
 ecological communities is focused on how temperature affects resource
 quantity. However, resource quality is also affected by warming, and
 changes in resource quality can have meaningful effects on the
 productivity of higher trophic levels. 2. Aquatic communities in
 particular are likely to affected by temperature-mediated shifts in
 resource quality because the nutritional value of algae is highly
 sensitive to temperature. For example, the production of healthful omega-3
 polyunsaturated fatty acids (n-3 PUFA) by algae often decreases with
 warming. 3. Documented decreases in algal PUFAs with warming have led to
 the hypothesis that global warming should lead to an overall decrease in
 productivity in aquatic communities. However, this hypothesis: a)
 potentially oversimplifies the relationship between algal PUFAs and
 temperature, and b) assumes that the nutritional requirements of consumers
 are not affected by temperature warming. Here we test these assumptions
 using a freshwater community (Scenedesmus algae, Daphnia zooplankton,
 Chaoborus insects). 4. We found that total algal PUFAs per unit cell size
 increased, but cell size decreased with warming, resulting no net effect
 of warming on PUFA per algal cell. We also found a negative relationship
 between algal neutral lipids and temperature. Daphnia fed 12˚C-reared
 algae maintained higher population sizes than those fed 20˚C or
 28˚C-reared algae, but the effect of algal food type diminished with
 increasing Daphnia rearing temperature. The indirect effects of
 cold-reared algae on the growth rate of Chaoborus predators were minor. 5.
 These data highlight the importance of investigating the effects of
 temperature on both resource quality and on the nutritional needs of
 consumers. Our results suggest that at warmer temperatures, consumer
 nutritional requirements may be reduced. We caution against broad claims
 that the negative relationship between some algal PUFAs and temperature
 should result in overall declines in aquatic productivity with ongoing
 climate warming.
description: This was a laboratory experiment. Please see the manuscript for
 details. 
description: All raw data used to create the results in the manuscript are
 included here.
DOI: 10.25338/b8gg92
title: Domestic cats (Felis catus) prefer freely available food over food that requires effort - corrected data

description: Contrafreeloading is the willingness of animals to work for food when
 equivalent food is freely available. This behavior is observed in
 laboratory, domesticated, and captive animals. However, previous research
 found that six laboratory cats failed to contrafreeload. We hypothesized
 that cats would contrafreeload in the home environment when given a choice
 between a food puzzle and a tray of similar size and shape. We also
 hypothesized that more active cats would be more likely to contrafreeload.
 We assessed the behavior of 17 neutered, indoor domestic cats (Felis
 catus) when presented with both a food puzzle and a tray across ten
 30-minute trials. Each cat wore an activity tracker, and all sessions were
 video recorded. Cats ate more food from the free feed tray than the puzzle
 (t(16) = 6.77, p &lt; 0.001). Cats made more first choices to approach
 and eat from the tray. There was no relationship between activity and
 contrafreeloading, and there was no effect of sex, age, or previous food
 puzzle experience on contrafreeloading. Our results suggest that cats do
 not show strong tendencies to contrafreeload in the home environment,
 although some cats (N = 4) ate most food offered in the puzzle or showed
 weak contrafreeloading tendencies (N = 5). Eight cats did not
 contrafreeload. Cats who consumed more food from the puzzle, consumed more
 food in general, suggesting a relationship between hunger and effort.
  Further research is required to understand why domestic cats,
 unlike other tested species, do not show a strong preference to work for
 food.
description: This data is from an observational study of cats; it includes
 data recorded by cat owners, as logged on an activity tracker worn by the
 cats, and from video data of the cats.
description: Data includes: demographics related to the
 cats (age, sex) the amount of food cats ate from two
 sources (food puzzle, tray) across 10 trials activity
 as measured by an activity tracker (Fitbark) choices
 made to approach and eat from the two food sources for 10 trials
 amount of time spent at the two food sources for 10
 trials
DOI: 10.5061/dryad.c59zw3r6d
title: Functional relationship between woody plants and insect communities in response to Bursaphelenchus xylophilus infestation in the Three Gorges Reservoir region

description: To study the effect of the invasion of Bursaphelenchus xylophilus on the
 functional relationship between woody plants and insect communities, the
 populations of tree species and insect communities were investigatived in
 the Masson pine forests with different infestation durations of B.
 xylophilus.
DOI: 10.6078/d1j12b
title: Data from: Patterns of fine-scale spatial genetic structure and pollen dispersal in giant sequoia (Sequoiadendron giganteum)

description: Research Highlights: Patterns of dispersal shape the distribution
 and temporal development of genetic diversity both within and among
 populations. In an era of unprecedented environmental change, the
 maintenance of extant genetic diversity is crucial to population
 persistence.  Background and Objectives: We investigate
 patterns of pollen dispersal and spatial genetic structure within
 populations of giant sequoia (Sequoiadendron
 giganteum).  Materials and Methods: The leaf genotypes
 of established trees from twelve populations were used to estimate the
 extent of spatial genetic structure within populations, as measured by the
 Sp statistic. We utilized progeny arrays from five populations to
 estimate mating parameters, the diversity of the pollen pool, and
 characteristics of pollen dispersal.  Results: Our
 research indicates that giant sequoia is predominantly outcrossing, but
 exhibits moderate levels of bi-parental inbreeding (0.155). The diversity
 of the pollen pool is low, with an average of 7.5 pollen donors per mother
 tree. As revealed by the Sp-statistic, we find significant genetic
 structure in ten of twelve populations examined, which indicates the
 clustering of related individuals at fine spatial scales. Estimates of
 pollen and gene dispersal indicate predominantly local dispersal, with the
 majority of pollen dispersal &lt;253 m, and with some populations
 showing fat-tailed dispersal curves, suggesting potential for
 long-distance dispersal.  Conclusions: The research
 presented here represent the first detailed examination of the
 reproductive ecology of giant sequoia, which will provide necessary
 background information for the conservation of genetic resources in this
 species. We suggest that restoration planting can mitigate potential
 diversity loss from many giant sequoia populations.
DOI: 10.5061/dryad.02v6wwq2c
title: Arabidopsis ovule primordium stages 0-I to 2-II, wild-type Col_0, Ws-4 and botero (bot1-7) mutant

description: This image resource describes the development of ovule primordia from
 stages 0-I to 2-I in 3D and at cellular resolution. The images were
 segmented using ImarisCell (BitplaneAG) and annotated as described in the
 associated manuscript Hernandez-Lagana et
 al. https://www.biorxiv.org/content/10.1101/2020.07.30.226670v3
description: Imaging
 of ovule primordia stained in whole-mount for cell boundary was done as
 described (Mendocilla-Sato, 2017) using a
 laser scanning confocal
 microscope Leica LCS SP8 equipped with a 63X glycerol
 immersion objective and HyD detectors. <strong>3D imaging and image processing (segmentation and labeling)</strong> Entire carpels were stained using the pseudo-Schiff propidium iodide (PS-PI) cell wall staining procedure providing excellent optical transparency for 3D imaging in depth in whole-mount. We described previously the manipulation, staining, mounting of the flower carpels and imaging procedures (Mendocilla-Sato, 2017). Cell-boundary based image segmentation was done using ImarisCell (Bitplane) as described in details previously (Mendocilla-Sato, 2017).  Each ovule was manually labelled in Imaris using customized Cell Labels for the different cell types and domains colored as shown in Figure 1<strong>. </strong>We defined the labels as follows:<strong> </strong> SMC (Spore Mother Cell): most apical central enlarged L2 cell. At stage 0-I, as enlargement is not always detected visually, the most apical L2 cell was then selected as candidate SMC (cSMC). L1:  epidermal cells L1 dome: most apical cells in contact with SMC L2/L3: cells below the epidermis. L2 and L3 were not distinguished originally. Apical domain: group of cells at the apex of the primordium and encompassing the SMC and direct neighbor cells. Basal domain: group of cells at the basis of the primordium below the apical domain and until, but not including cells of the placental surface. At stages 0-I and 0-II only an apical domain is defined. A basal domain appears only starting stage 0-III. CC (Companion Cell): L2 cells in apical domain in contact with the SMC with an elongated shape (as judged in ovule longitudinal median section using the “clipping plane” IMARIS tool). SMC contact: cells in contact with the SMC. Semi-automated segmentation requiring user input and manual labelling can be error prone. To reduce the error rate, the 92 images were segmented and labeled by one author, but verified and curated by two others.
DOI: 10.5061/dryad.0cfxpnw16
title: Field-based ecological studies to assess prospective biological control agents for invasive alien plants: an example from giant rat’s tail grass

description: 1. Biological control (biocontrol) of invasive alien plants is a widely
 utilised weed management tool. Prospective biocontrol agents are typically
 assessed through host-specificity testing and pre-release efficacy studies
 performed in quarantine. However, rearing of the potential biocontrol
 agents and/or test plants is often difficult or impossible under
 quarantine conditions. Moreover, practitioners may attain
 laboratory-artefacts in quarantine, which may result in the potential
 agent being needlessly rejected. Field-based studies in the weed’s
 indigenous distribution could overcome these issues. 2. Sporobolus
 pyramidalis and Sporobolus natalensis (giant rat’s tail grass; Poaceae)
 are indigenous in Africa but have become problematic invasive alien plants
 in Australia. A previous biocontrol programme was terminated because the
 candidate agent could not be reared and tested in quarantine. We performed
 field-based host-specificity and efficacy studies for prospective
 biocontrol agents in South Africa (indigenous distribution). Forty-seven
 non-target grass species were sampled during host-specificity assessments.
 Candidate agent efficacy was estimated based on damage to the target
 weeds, for each host-specific candidate individually and in combination
 with other host-specific candidates. 3. Three species of endophagous wasps
 were deemed host-specific. Efficacy assessments identified an undescribed
 stem-boring wasp (Tetramesa sp.) species as the most damaging candidate. A
 second Tetramesa species was much less damaging alone but had a cumulative
 impact on the plant in combination with the more damaging Tetramesa
 species. Both Tetramesa species are recommended for importation into
 quarantine in Australia for confirmatory host-specificity testing with a
 significantly reduced test plant list. 4. Synthesis and applications:
 Similar field-based assessments in the indigenous distribution of weeds
 targeted for biocontrol could be included in future programmes. Where
 rearing of potential agents and/or test plants is difficult or impossible
 under quarantine conditions, our field-based method provides an
 alternative. Where quarantine-based testing is feasible, this method
 ensures that only candidates that have passed an ecologically realistic
 host-specificity and potential efficacy screening are imported into
 quarantine. This may reduce the number of agents that are imported and the
 length of time each agent is kept in quarantine. This is advantageous
 because quarantine space is highly valuable and is usually a limiting
 factor in pre-release assessments of biocontrol agents.
DOI: 10.5061/dryad.crjdfn336
title: Metabolic rate and behavioral traits in Salmo trutta

description: The behavior of organisms can be subject to human induced selection such
 as that arising from fishing. Angling is expected to induce mortality on
 fish with bold and explorative behavior, which are behaviors commonly
 linked to a high standard metabolic rate. We studied the transgenerational
 response of brown trout (Salmo trutta) to angling-induced selection by
 examining the behavior and metabolism of 1-year-old parr between parents
 that were or were not captured by experimental fly fishing. We performed
 the angling selection experiment on both a wild and a captive population,
 and compared the offspring for standard metabolic rate and behavior under
 predation risk in common garden conditions. Angling had
 population-specific effects on risk taking and exploration tendency, but
 no effects on standard metabolic rate. Our study adds to the evidence that
 angling can induce transgenerational responses on fish personality.
 However, understanding the mechanisms of divergent responses between the
 populations requires further study on the selectivity of angling in
 various conditions.
description: Metabolic rate raw data: Oxygen saturation was
 measured in % of air saturation using two-point-calibrated DAQ-PAC-WF4
 system with Sensor spot mini sensors and recorded every second in AutoResp
 software (Loligo Systems). Water temperature was measured using the Pt1000
 temperature probe placed in the respirometer tank (Loligo Systems). Data
 was reformatted into Fishresp format for analysis.
description: Note on metabolic rate raw data: The raw data
 are in files with "_fixed" ending, these were processed as in
 the scripts provided in Github (see publication) to obtain data for
 analysis in Fishresp (fixed_conv ending). Intermediate data files also
 provided, as well as Sample IDs to combine data from chambers to fish PIT
 IDs and other information.
DOI: 10.5061/dryad.5dv41ns5c
title: Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo

description: Horizontal gene transfer, mediated by conjugative plasmids, is a major
 driver of the global rise of antibiotic resistance. However, the relative
 contributions of factors that underlie the spread of plasmids and their
 roles in conjugation in vivo are unclear. To address this, we investigated
 the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing
 plasmids in the absence of antibiotics in vitro and in the mouse
 intestine. We hypothesised that plasmid properties would be the primary
 determinants of plasmid spread and that bacterial strain identity would
 also contribute. We found clinical Escherichia coli strains natively
 associated with ESBL-plasmids conjugated to three distinct E. coli strains
 and one Salmonella enterica serovar Typhimurium strain. Final
 transconjugant frequencies varied across plasmid, donor, and recipient
 combinations, with qualitative consistency when comparing transfer in
 vitro and in vivo in mice. In both environments, transconjugant
 frequencies for these natural strains and plasmids covaried with the
 presence/absence of transfer genes on ESBL-plasmids and were affected by
 plasmid incompatibility. By moving ESBL-plasmids out of their native
 hosts, we showed that donor and recipient strains also modulated
 transconjugant frequencies. This suggests that plasmid spread in the
 complex gut environment of animals and humans can be predicted based on in
 vitro testing and genetic data.
DOI: 10.5061/dryad.ngf1vhhsw
title: Shape of species climate performance curves affects community response to climate change

description: Understanding how community composition is reshaped by changing climate is
 important for interpreting and predicting patterns of community assembly
 through time or across space. Community composition often does not
 perfectly correspond to expectations from current environmental
 conditions, leading to community-climate mismatches. Here, we combine data
 analysis and theory development to explore how species climate response
 curves affect the community response to climate change. We show that
 strong mismatches between community and climate can appear in the absence
 of demographic delays or limited species pools. Communities simulated
 using species response curves showed temporal changes of similar magnitude
 to those observed in natural communities of fishes and plankton,
 suggesting no overall delays in community change despite substantial
 unexplained variation from community assembly and other processes. Our
 approach can be considered as a null model that will be important to use
 when interpreting observed community responses to climate change and
 variability.