cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qjq2bvqgd
title: Asymmetric cross-strain protection for amphibians exposed to a fungal-metabolite prophylactic treatment

description: Chytridiomycosis, an infectious disease of amphibians caused by the fungal
 pathogen Batrachochytrium dendrobatidis (Bd), poses an imminent
 conservation threat. The global spread of Bd has led to mass mortality
 events in many amphibian species, resulting in at least 90 species’
 extinctions to date. Exposure to Bd metabolites (i.e., non-infectious
 antigenic chemicals released by Bd) partially protects frogs during
 subsequent challenges with live Bd, suggesting its use as a prophylactic
 treatment and potential vaccine. However, we do not know whether Bd
 metabolite exposure protects against strains beyond the one used for
 treatment. To address this knowledge gap, we conducted a 3x2 experiment
 where we exposed adult Cuban treefrogs, Osteopilus septentrionalis, to one
 of three treatments (Bd metabolites from California-isolated strain
 JEL-270, Panamá-isolated strain JEL-419, or an artificial spring water
 control) and then challenged individuals with live Bd from either strain.
 We found that exposure to Bd metabolites from the California-isolated
 strain significantly reduced Bd loads of frogs challenged with the live
 Panamá-isolated strain, but no other treatments were found to confer
 protective effects. These findings demonstrate asymmetric cross-protection
 of a Bd metabolite prophylaxis and suggests that work investigating
 multiple, diverse strains is urgently needed.
description: See main text.
DOI: 10.5061/dryad.ngf1vhhv2
title: How to cope with drought and not die trying: drought acclimation across tree species with contrasting niche breadth

description: Worldwide drought events have been reported to cause tree growth decline
 and mortality, thus altering the carbon (C) balance of forest ecosystems.
 While most of the attention has been focused on the physiological
 mechanisms associated with drought-induced tree responses of a few species
 at specific locations, the ecological attributes of these species, like
 their niche breadth, may be also important in determining species’
 sensitivity or resilience to drought. We postulated that wide-niche
 breadth tree species should be more drought-resilient than narrow-niche
 breadth species. 2. Using the most severe 2015-2016 El Niño drought event
 in the last 70 years in Patagonia, we determined pre- and post-drought
 growth (BAI, basal area increment), C reserves in the form of
 non-structural carbohydrates (NSCs = starch and soluble sugars), wood
 isotope (δ13C, iWUE and δ18O) signaling, and xylem anatomy (mean vessel
 diameter, mvd) in eight angiosperm tree species of contrasting niche
 breadth across a sharp precipitation gradient in southern Chile. 3. All
 species responded in unison after the drought with a
 non-water-conservative response, maintaining BAI and NSCs concentrations,
 decreasing δ13C, and increasing both mvd and the soluble sugars:NSCs ratio
 relative to pre-drought time. Contrary to previous results reporting
 species-specific drought responses, our results show unequivocally a
 functional coordination of organisms’ vital traits associated with a
 non-water-conservative strategy, and a drought-induced acclimation based
 on starch conversion into soluble sugars in all of the tree species we
 examined, regardless of their niche breadth and habitat preference. 4. We
 state that abiotic drivers such as drought may have selected similar
 interspecific responses provided that they operate at the community level
 rather than at the species level. These findings mark the need to revise
 current views about the ultimate interspecific functional coordination of
 organisms’ vital traits when facing more frequent and intensive drought
 events.
description: Data collected across broad-leaved tree species across a sharp
 precipitation gradient in Patagonia, Chile. The data was collected in situ
 before and after the occurrence of a unprecedent drought in the 2015-2016
 growing season.  Data providing values for wood density
 (g cm<sup>-3</sup>), non-structural carbohydrates (mg
 g<sup>-1</sup>), starch (mg g<sup>-1</sup>),
 soluble sugars (mg g<sup>-1</sup>) and basal area increment
 (bai, cm<sup>2</sup>).
DOI: 10.25338/b81w61
title: Fighting for curb space: Micro-simulation

description: This study conducted a comprehensive literature review on several topics
 related to curb space management, discussing various users (e.g.,
 pedestrians, bicycles, transit, taxis, and commercial freight vehicles),
 summarizing different experiences, and focusing the discussion on Complete
 Street strategies. Moreover, the authors reviewed the academic literature
 on curbside and parking data collection, and simulation and optimization
 techniques. Considering a case study around the downtown area in San
 Francisco, the authors evaluated the performance of the system with
 respect to a number of parking behavior scenarios. The authors developed a
 parking simulation in SUMO following a set of parking behaviors (e.g.,
 parking search, parking with off-street parking information availability,
 double-parking). These scenarios were tested in three different (land
 use-based) sub-study areas representing residential, commercial and
 mixed-use. The data contains the GIS information of the three study areas,
 and the SUMO scripts.
description: The team used public information about land uses and
 socio-demographic characteristics in the study area.
 Trips were taken from the Metropolitan Transportation Council
 Activity Based Model in the Bay Area, and transferred to SUMO (and an
 intermediate step in MatSIM). For freight, the team implemented trip
 generation models for commercial establishments.
DOI: 10.5061/dryad.mpg4f4r0g
title: Differential impacts of alternate primary producers on carbon cycling

description: Disturbance impacts the spatial distribution of primary producers, which
 can have cascading effects on ecosystem function. The lower-intertidal
 zone on the rocky shores of the Pacific Northwest is one such place where
 wave energy creates a mosaic-like distribution between two assemblages:
 surfgrass (Phyllospadix scouleri) meadows and macroalgal forests dominated
 by kelp. We simulated wave disturbance by experimentally removing patches
 of surfgrass monocultures, resulting in a macroalgal assemblage with
 increased diversity, biomass, and net primary productivity in the
 following year. While surfgrass had a higher C:N compared to macroalgal
 assemblages, macroalgal assemblages achieved a higher biomass, fixed
 carbon at a faster rate, and released more dissolved organic carbon (DOC)
 during photosynthesis. Thus, despite similar standing amounts of carbon,
 macroalgal assemblages have increased carbon turnover – from fixation to
 DOC release. Comparative photophysiology indicated that surfgrasses have a
 competitive advantage over other macrophytes at low-light levels, allowing
 them to persist when disturbance is reduced. Unexpectedly, disturbance in
 this system increased the potential for carbon sequestration when
 surfgrass monocultures were replaced by diverse macroalgae.
DOI: 10.5061/dryad.hdr7sqvj9
title: Data from: Experimentally induced flight costs do not lead to increased reliance on supplemental food in winter by a small songbird

description: Each year hundreds of millions of people intentionally feed wild animals
 throughout the world. For decades, concerns have persisted regarding the
 potential for intentional feeding to promote dependency on
 human-supplemented food, particularly during energetically demanding
 periods of the annual cycle. In this study, we evaluated whether
 individuals subjected to experimentally increased flight costs responded
 by increasing their use of supplemental feeders in a wild, free-ranging
 population of the Black-capped Chickadee (Poecile atricapillus). We
 subjected 67 RFID-tagged chickadees to one of three handicapping
 treatments (heavy feather-clipping, light feather-clipping, or unclipped
 controls) and then evaluated feeder use of each individual relative to
 their pre-treatment level. Contrary to predictions, we found that
 chickadees in both feather-clipping treatments exhibited a short-term
 reduction in feeder use, returning to feeding levels of unmanipulated
 controls within approximately 2 weeks of treatment implementation.
 Similarly, experimental feather-clipping treatments had little influence
 on changes in the number of feeders used or on the timing of feeder visits
 across the daily cycle, relative to controls. Our results indicate that
 experimental handicapping of chickadees led to relatively minor and
 transient changes in the use of supplemental food with no evidence that
 handicapped individuals increased their reliance on supplemental bird
 feeders. These findings suggest that recreational bird feeding is unlikely
 to lead to feeder dependency in small songbirds during winter, although
 additional research on this topic should be a priority given the global
 footprint of intentional feeding of wildlife.
DOI: 10.5061/dryad.2jm63xspv
title: Data: Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere

description: Introduced species have become an increasingly common component of
 biological communities around the world. A central goal in invasion
 biology is therefore to identify the demographic and evolutionary factors
 that underlie successful introductions. Here we use whole genome
 sequences, collected from populations in the native and introduced ranges
 of the African fig fly, Zaprionus indianus, to quantify genetic
 relationships among them, identify potential sources of the introductions,
 and test for selection at different spatial scales. We find that
 geographically widespread populations in the western hemisphere are
 genetically more similar to each other than to lineages sampled across
 Africa, and that these populations share a mixture of alleles derived from
 differentiated African lineages. Using patterns of allele-sharing and
 demographic modelling we show that Z. indinaus have undergone a single
 expansion across the western hemisphere with admixture between African
 lineages predating this expansion. We also find support for selection that
 is shared across populations in the western hemisphere, and in some cases,
 with a subset of African populations. This suggests either that parallel
 selection has acted across a large part of Z. indianus’s introduced range;
 or, more parsimoniously, that Z. indianus has experienced selection early
 on during (or prior-to) its expansion into the western hemisphere. We
 suggest that the range expansion of Z. indianus has been facilitated by
 admixture and selection, and that management of this invasion could focus
 on minimizing future admixture by controlling the movement of individuals
 within this region rather than between the western and eastern hemisphere.
description: Data tables summarise results produced as part of a study of
 genetic differentiation among populations of the African fig fly,
 Zaprionus indianus. Please see ReadMe file for details of what is
 contained within each file.
DOI: 10.5281/zenodo.18397149
title: Organic carbon and nitrogen geochemistry of Taiwan and the northern South China Sea

description: While chemical weathering of silicate rocks of low-latitude arc–continent collisions has been hypothesized as a driver of global cooling since the Neogene, the role of physical weathering on carbon export and burial has largely been overlooked. In mid- to low-latitude regions, monsoon and tropical cyclone precipitation drive intense physical erosion that may contribute to terrestrial carbon export and nutrient-stimulated marine productivity. To evaluate the influence of physical erosion of an arc-continent collision on organic carbon sequestration in the adjacent ocean basin, we analyse late Miocene to early Pleistocene sedimentary and geochemical records from the Taiwan Western Foreland Basin and time-equivalent records from the northern South China Sea. Total organic carbon (TOC) and total nitrogen (TN) concentrations were determined from pulverized rock samples collected from outcrops of the Taiwan Western Foreland Basin (Chinshui Shale and the Cholan Formation), and sediment samples collected from cored intervals from the northern South China Sea (ODP Site 1146 and 1148). Samples were analyzed using elemental analysis and rock-eval pyrolysis. Organic carbon isotopic compositions (δ13Corg, ‰ relative to Vienna Pee Dee Belemnite) were also measured for both outcrop and sediment core samples by flash combustion on an elemental analyser (EA) coupled to an isotope-ratio mass spectrometer (IRMS).
DOI: 10.5281/zenodo.18397150
title: Organic carbon and nitrogen geochemistry of Taiwan and the northern South China Sea

description: While chemical weathering of silicate rocks of low-latitude arc–continent collisions has been hypothesized as a driver of global cooling since the Neogene, the role of physical weathering on carbon export and burial has largely been overlooked. In mid- to low-latitude regions, monsoon and tropical cyclone precipitation drive intense physical erosion that may contribute to terrestrial carbon export and nutrient-stimulated marine productivity. To evaluate the influence of physical erosion of an arc-continent collision on organic carbon sequestration in the adjacent ocean basin, we analyse late Miocene to early Pleistocene sedimentary and geochemical records from the Taiwan Western Foreland Basin and time-equivalent records from the northern South China Sea. Total organic carbon (TOC) and total nitrogen (TN) concentrations were determined from pulverized rock samples collected from outcrops of the Taiwan Western Foreland Basin (Chinshui Shale and the Cholan Formation), and sediment samples collected from cored intervals from the northern South China Sea (ODP Site 1146 and 1148). Samples were analyzed using elemental analysis and rock-eval pyrolysis. Organic carbon isotopic compositions (δ13Corg, ‰ relative to Vienna Pee Dee Belemnite) were also measured for both outcrop and sediment core samples by flash combustion on an elemental analyser (EA) coupled to an isotope-ratio mass spectrometer (IRMS).
DOI: 10.5061/dryad.ns1rn8pt4
title: Zostera marina microsatellite and environmental data

description: Microsatellite data for Zostera marina, sea otter occupancy
 information, and environmental data from the west coast of
 British Columbia, Canada.
description: The methods detailing sample collection, storage, DNA extraction,
 and genotyping, and collectin of environmental data, are detailed in our
 manuscript, Foster et al., in revision
 (2021), <em>Science</em>.
description: Please review the ReadMe.pdf file.
DOI: 10.5061/dryad.2rbnzs7np
title: Species-level coral bleaching data for Maldives and GBR

description: Response to coral bleaching for 7368 coral colonies exposed to similar
 levels of temperature stress at a similar depth of occurrence and similar
 subsequent mortality. Collected in situ following  moderate
 thermal bleaching events in the GBR in 2002 and the Maldives in 2016. Data
 gives species, site, depth of occurence and bleaching response which was
 scored by tissue colour.   
description: For the GBR in 2002 and the MA in 2016, sea surface temperatures
 (SSTs) exceeded bleaching thresholds over wide areas for several weeks
 (NOAA, 2021), resulting in mortalities at some sites to 68% and 86%
 respectively (Cowburn et al., 2019; Done et al. 2003). We restricted our
 analyses to sites with a DHW of between 4 and 7, which is currently
 considered moderate bleaching stress (NOAA 2021, Skirving et al., 2019).
 Ten locations (30 sites) from the Maldives were included, all within the
 large (~2000 km<sup>2</sup>) Ari Lagoon complex on high
 coral-cover reef slopes adjacent to small islands with little or no human
 populations (Figure 1a). Sites were protected from most ocean swells and
 extended to a sandy base at 20-30 m depth. Included sites for the GBR (14
 locations, 22 sites) were also situated on high coral-cover reef slopes
 within the large GBR lagoon complex (Figure 1b). These sites were either
 adjacent to small islands or on the back, lagoon or southern slopes of mid
 or outer shelf platform reefs. At each site, timed
 surveys using SCUBA or snorkel dives of 45-80 minutes duration were
 conducted, recording bleaching responses and recent mortality of
 individuals according to standard methods. Species identifications were
 mostly made <i>in situ, </i>with high-resolution macro
 photographs or small samples taken from problematic morphotypes (under
 permit) for later analysis by comparison with material available in the
 Queensland Museum, consultation with relevant experts and reference to
 standard texts (see Supporting Information for details). Both datasets
 were converted to current valid species (Hoeksema & Cairns, 2019).
 For certain genera (e.g. <i>Montipora, Porites, Goniopora
 </i>and <i>Cycloseris</i>) it was not possible to
 accurately assign a species or morphotype <i>in situ, </i>so
 these were assessed as grouped species and only considered in a
 supplementary analysis.
description: See readme file
DOI: 10.5061/dryad.9ghx3ffhj
title: Knifefish turning performance during forward swimming

description: Rapid turning and swimming contribute to ecologically
 important behaviors in fishes such as predator avoidance,
 prey capture, mating, and the navigation of complex
 environments. For riverine species, such as knifefishes, that are
 commonly challenged by turbulent flows,
 turning control may be effective for
 counteracting adverse locomotive perturbations. Most research on
 fish maneuvering focuses on fish with traditional fin and body
 morphologies, which primarily use body bending and the
 pectoral fins during turning. However, it is uncertain
 how fishes
 with uncommon morphologies, are able
 to achieve sudden and controllable turns. Here
 we studied the turning performance and the turning hydrodynamics
 of the Black ghost knifefish (Apteronotus albifrons, N=6) which
 has an atypical elongated ribbon fin. Fish were filmed while
 swimming forward at ~2 BL s-1 and feeding from a fixed feeder (control)
 and an oscillating feeder (75 Hz) at two different amplitudes. 3D
 kinematic analysis of the body revealed the highest pitch angles and
 lowest body bending coefficients occurred during steady swimming. Low
 pitch angle, high maximum yaw angles and large body bending coefficients
 were characteristic of small and large turns. Asynchrony in pectoral fin
 use was low during turning, however ribbon fin wavelength, frequency, and
 wave speed were greatest during large turns.  Digital particle
 image velocimetry (DPIV) showed larger counter-rotating
 vortex pairs produced during turning by the
 ribbon-fin in comparison to vortices rotating in the same
 direction during steady swimming. Our results highlight the
 ribbon fin’s role in controlled rapid turning through modulation of
 wavelength, frequency, and wave speed.
description: This dataset was collected using 3D highspeed videography filming
 at 250 frames per second in the lateral and ventral views. Data analyzed
 using Matlab and R. 
description: IndividualxTreatment_HawkinsJimenezSanford_2021.xlsx [Data set
 used for statistical analysis including the means of each fish (N=6) per
 each treatment.]
 AllObservations_HawkinsJimenezSanford_2021.xlsx [Data set with
 compiled means from each digitization sequence for each treatment for each
 fish (N=6)].
 RawDataSet_fishxtreatment_HawkinsJimenezSanford_2021.xlsx [Data
 set with all calibrated digitization coordinates in the x, y, and z planes
 for each analyzed sequence. Small turn files can be found in sheets 1- 43,
 large turn files can be found in sheets 44-80, and steady swimming files
 can be found in sheets 81- 118. Point 1 (tip of snout], Point 2 (end of
 head), Point 3 (body point in between pectoral fins), Point 4 (body
 point), Point 5 (body point), Point 6 (caudal peduncle), Point 7 (tip
 caudal fin), Point 8 (left pectoral fin tip), Point 9 (left pectoral fin
 base), Point 10 (right pectoral fin tip), Point 11 (right pectoral fin
 base), Point 12 (ribbon fin tip), Point 13 (ribbon fin base corresponding
 to Point 12), Point 14 (ribbon fin tip of a contiguous wave).]
DOI: 10.5061/dryad.ffbg79cv8
title: Enduring evolutionary embellishment of cloudinids

description: The Ediacaran–Cambrian transition and the following Cambrian Explosion are
 among the most fundamental events in the evolutionary history of animals.
 Understanding these events is enhanced when phylogenetic linkages can be
 established among animal fossils across this interval and their trait
 evolution monitored. Doing this is challenging because the fossil record
 of animal lineages that span this transition is sparse, preserved
 morphologies generally simple, and lifestyles in the Ediacaran and
 Cambrian quite different. Here we identify derived characters linking some
 members of an enigmatic animal group, the cloudinids, which first appeared
 in the late Ediacaran, to animals with cnidarian-affinity from the
 Cambrian Series 2 and the Miaolingian. Accordingly, we present the first
 case of an animal lineage represented in the Ediacaran that endured and
 diversified successfully throughout the Cambrian Explosion by embellishing
 its overall robustness and structural complexity. Among other features,
 dichotomous branching, present in some early cloudinids, compares closely
 with a cnidarian asexual reproduction mode. Tracking this morphological
 change from late Ediacaran to the Miaolingian provides a unique glimpse
 into how a primeval animal group responded to the Cambrian Explosion.
description: Data matrix has collected from several published research
 articles. TNT (ver.15) was applied to run the matrix
 for phylogenetic tree.