cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wwpzgmsq7
title: Effects of long-term fixed fire regimes on African savanna vegetation biomass, vertical structure and tree stem density

description: Fire plays an integral role in shaping the vegetation structure of savanna
 ecosystems. However, effects of fire regime characteristics, such as
 frequency and season of burn, on savanna vegetation structure, biomass and
 tree abundance across landscape types are largely unknown. We used
 high-resolution airborne Light Detection and Ranging (LiDAR) to
 investigate the long-term effects of fire manipulation on savanna
 vegetation in Kruger National Park, South Africa. We analysed the effects
 of fire exclusion and experimental burns every 1, 2, 3, 4 and 6 years and
 during different seasons on aboveground biomass (AGB), tree stem densities
 and vegetation vertical height profiles across a rainfall gradient and on
 contrasting geologies. Across savanna types, and especially in drier
 savannas, fire season was more influential for constraining AGB than was
 fire frequency. Plots experiencing fires during the late- and mid-dry
 season had 44.50% and 43.60%, respectively, lower AGB relative to unburnt
 plots than wet-season fires. However, in mesic savannas, fire frequency
 interacted with fire season to influence AGB: plots subjected to high
 frequency, dry season fires had 55.35% lower AGB than unburnt plots,
 whereas plots burnt in the wet season at lower frequencies had lower AGB
 (24.40% lower than unburnt plots) than plots subjected to high frequency,
 wet-season fires (13.74% lower AGB than unburnt plots). Fire regimes had
 variable effects on tree densities, and effects varied with savanna type.
 Woody vertical vegetation profiles showed the largest differences in
 response to dry season fires, with the greatest divergence in vegetation
 height classes &lt; 5m.  Synthesis and applications.
 Understanding the influence of fire regimes on vegetation structure has
 important implications for the management of savanna heterogeneity, and
 for predicting trajectories of change in savanna vegetation as fire
 regimes vary with climate change. We show that the magnitude of the effect
 of fire on woody vegetation structure varies with savanna context. Our
 results suggest that heterogeneous vegetation structure can be achieved by
 applying fires in the dry season in mesic savannas, whereas in dry
 savannas, variation in fire regimes is less consequential for constraining
 biomass accumulation and altering vegetation structure.
description: The dataset consists of vegetation metrics (aboveground biomass,
 tree density, aboveground biomass change, vertical vegetation profiles)
 derived from drone-based LiDAR.
DOI: 10.5061/dryad.9zw3r22k6
title: Henslow's Sparrow shows positive response to prescribed fire rotation data

description: We examined Henslow’s Sparrow (Centronyx henslowii) response to prescribed
 fire at 32 grasslands at Big Oaks National Wildlife Refuge in southeastern
 Indiana from 1999–2009. We burned grasslands in the spring between 1999
 and 2007 and monitored Henslow’s Sparrows for up to 4 years after
 treatment. We used linear mixed models to analyze our data. Henslow’s
 Sparrow counts were correlated with time since prescribed fire and
 grassland size. The estimated changes in mean Henslow’s Sparrow density
 relative to pre-burn densities were -0.19, 1.15, 0.74, and -0.68 birds per
 hectare for 1 to 4 breeding seasons after a spring burn, respectively. We
 found that Henslow’s Sparrows preferred larger grasslands both during the
 first breeding season after prescribed fire, when vegetation was presumed
 to possess less litter and structural density, and during the fourth
 breeding season after fire, when vegetation was presumed to be a more
 ideal composition, but preferred smaller grasslands in the interim. Thus,
 grassland size shapes the magnitude of Henslow’s Sparrow population
 response to fire, with populations in smaller grasslands experiencing
 greater amplitude changes. Larger grasslands might provide more habitat
 diversity following prescribed fire, attenuating population change. On
 average, Henslow’s Sparrows responded positively to prescribed fire in a
 network of grasslands and cumulative net change in densities were highest
 three breeding seasons after a burn, suggesting that maintaining this burn
 frequency would be beneficial to Henslow’s Sparrow abundance.
DOI: 10.5061/dryad.2547d7wwk
title: Data from: Increased aridity is associated with stronger tradeoffs in ponderosa pine vital functions

description: Trees must allocate resources to core functions, like growth, defense, and
 reproduction. These allocation patterns have profound effects on forest
 health, yet little is known about how core functions trade off over time,
 and even less is known about how a changing climate will impact tradeoffs.
 We conducted a 21-year survey of growth, defense, and reproduction in 80
 ponderosa pine individuals spanning 8 populations across environmental
 gradients along the Colorado Front Range, USA. We used linear mixed models
 to describe tradeoffs among these functions and to characterize
 variability among and within individuals over time. Growth and defense
 were lower in years of high cone production and local drought conditions
 amplified year-to-year tradeoffs between reproduction and growth, where
 trees located at sites with hotter and drier climates showed stronger
 tradeoffs between reproduction and growth. Our results support the
 environmental stress hypothesis of masting, which predicts that greater
 interannual variation in tree functions is associated with more marginal
 environments, such as those that are prone to drought. With warming
 temperatures and increased exposure to drought stress, trees will be faced
 with stronger interannual tradeoffs, which could lead to further decreases
 in growth and defensive efforts, ultimately increasing risks of mortality.
description: Data includes R code and datasets to reproduce figures and
 results from the manuscript titled: "Increased aridity is associated
 with stronger tradeoffs in ponderosa pine vital functions"
 Data are counts of annual cone production from <em>Pinus
 ponderosa</em> across the Colorado Front Range, USA, from 80 trees
 and 8 sites, reconstructed using cone scars from the time period
 2000-2020. Data also includes xylem growth measurements (taken from 12mm
 and 5mm cores), resin duct (total resin area, relative duct area, mean
 duct size), average stable carbon isotope data of each tree, and local
 site climate. See the readme file for full description of the
 files. 
description: We place no restrictions on the use of these data but encourage
 those interested in working with them to contact Angela Gonzalez at angiedgonzalez@gmail.com R scripts (.r) can be executed using R software and viewed in standard text editors. Tabular data (.csv, .xlsx) can be opened in MS Excel or open-source alternatives.
DOI: 10.25338/b8kp92
title: 2023 California Community Water System institutional type update

description: This data set builds directly on the original "Organizational
 structure and institutional types of community water systems in
 California" data set published in October 2021 by Dr. Kristin Dobbin
 and Dr. Amanda Fencl which reflected active Community Water Systems in
 California as of December 2018 (you can find this original data on Dryad
 under the following
 DOI: https://doi.org/10.25338/B8NS7Z). This 2023 update
 provides a current snapshot of the organizational and institutional
 structures of active California Community Water Systems with improvements
 to the accuracy and granularity of the data as we have further developed
 our understanding of these topics through this and other projects. See the
 accompanying README file for a complete breakdown of all changes and
 improvements.
DOI: 10.25345/c5xg9fq8s
title: MassIVE MSV000100616 - Skin Mucus Proteoforms of Barramundi
title: Skin mucus samples from male and female barramundi
DOI: 10.5061/dryad.41ns1rnk6
title: Data from: Convergent avialan brain morphology in Sinovenator (Troodontidae, Theropoda)

description: Sinovenator changii IVPP V20378 is a troodontid theropod dinosaur from the
 Early Cretaceous strata in Liaoning, northeastern China. The specimen is a
 nearly complete 3D-preserved skeleton. The postcranial elements are in
 sleeping posture and the skull is isolated from the rest. The skull
 suffered only slight deformation and distortion, completely preserving
 most of its elements except the left postorbital, parietal, and squamosal.
 The dataset comprises three .stl files of the skull, brain endocast, and
 inner ear of Sinovenator changii IVPP V20378. 
description: The skull and postcranial skeleton of this specimen were scanned
 separately at the Institute of Vertebrate Paleontology and
 Paleoanthropology, Beijing, China. The scanning was carried out using the
 225 kV micro-computerized tomography (developed by the Institute of High
 Energy Physics, Chinese Academy of Sciences (CAS)) at the Key Laboratory
 of Vertebrate Evolution and Human Origins, CAS. The specimen was scanned
 with a beam energy of 100 kV and a flux of 100 mA at a resolution of 61 μm
 per pixel using a 360° rotation with a step size of 0.5° and an unfiltered
 aluminum reflection target. The total dataset of 1,536 slices was
 reconstructed using two-dimensional reconstruction software MOCUPY
 developed by the Institute of High Energy Physics, CAS. The segmentation
 and rendering of the digital models were conducted in Mimics 19.0
 (Materilise, Belgium). The .stl files are directly exported from Mimics
 19.0.
description: # The skull and endocranium CT reconstruction of Sinovenator changii IVPP
 V20378 ## Description of the data and file structure There are three .stl
 files in the dataset. They are 3D reconstruction renderings of skull,
 brain endocast, and inner ear of the troodontid dinosaur Sinovenator
 changii, specimen number IVPP V20378. A .nex tree file including 51 taxa
 that was used in this study and related cranial endocast landmark data in
 .txt are also included here. Detail about data collection can be found in
 the manuscript. Sinovenator_Skull_001.stl Sinovenator_Brain_1221.stl
 Sinovenator_Inner_ear_1221.stl Sinovenator.txt SinovenatorTree.nex ##
 Code/Software The 3D reconstruction was conducted in software Mimics 19.0
 (Materilise, Belgium), then rendered models were directly exported as .stl
 files.
DOI: 10.5061/dryad.f7m0cfz24
title: Nestling growth rate and food consumption increases under experimentally prolonged day length in a New World Sparrow

description: When evaluating avian reproduction, life history theory examines the
 trade-offs between parental effort, the number and size of offspring, and
 the rate of nestling development. The growth rates and body sizes of
 developing birds vary geographically and can diverge with both latitude
 and migratory strategies. In terms of offspring size, growth rate can
 deviate in nestlings of the same or similar species due
 to the correlated influences of weather events,
 predation pressure, food availability, number of nestmates, and parental
 provisioning. Furthermore, a longer photoperiod for species nesting at
 higher latitudes increases the duration over which a nestling can be fed
 each day, and increased nestling provisioning has been positively
 correlated with growth rate. Whether the amount of time in which a bird is
 fed during development drives this variation in growth rate and morphology
 is unknown. By removing supplemental environmental stressors (e.g., food
 availability, weather, predation pressure) and standardizing feeding rate
 and environment, we explored the influence of daily duration of nestling
 provisioning on dark-eyed junco (Junco hyemalis) nestlings. We hand-reared
 65 chicks of a sedentary junco subspecies (J. h. carolinensis) under both
 their natural photoperiod and the longer photoperiod of a closely related
 migratory subspecies (J. h. hyemalis) and compared growth rate, mass,
 morphology, and the amount of food consumed. Average growth rate, fasted
 mass, wing length, and total daily food consumption were all greater in
 birds hand-reared under the longer, more northern photoperiod treatment.
 These findings suggest that increased daily photoperiod at higher
 latitudes may allow for greater total food provisioning and thus may play
 a role in the ability of parents in compressed breeding seasons to produce
 high-quality offspring. This points to a trade-off between provisioning
 effort and nestling growth rate in lower latitude (shorter photoperiod)
 populations and points to an important role of developmental plasticity on
 growth rate and morphology.
DOI: 10.7275/0gks-fs24
title: Pesticide residues in honey: Agricultural landscapes and commercial wax foundation sheets as potential routes of chronic exposure for honey bees

description: Pesticides pose significant threats to pollinators, and honey bees are frequently exposed through foraging and beekeeping practices. We assessed honey bee pesticide exposure by analyzing 92 pesticide residues in honey from 30 hobbyist apiaries across Massachusetts, along with store-bought honey and commercial wax foundation. For all samples, we calculated the risk of multiresidue toxicity to honey bees and assessed the role of landscape composition in predicting pesticides in local honey. Both honey and wax contained multiple pesticides, particularly neonicotinoids and piperonyl butoxide. Store-bought honey accumulated at least two times more residues than local but did not differ significantly in toxicity. Overall, honey toxicity levels remained below thresholds of concern for bees and human consumption. Although our study had low agricultural land (~6 %), croplands were positively correlated with pesticides in honey, while wetlands (~ 15 %) were negatively correlated. Additionally, our study suggests that commercial wax exacerbates pesticide exposure.
DOI: 10.5061/dryad.zcrjdfnhx
title: Reciprocated competition between two forest carnivores drives dietary specialization

description: Competition shapes animal communities, but the strength of the interaction
 varies spatially depending on the availability and aggregation of
 resources and competitors. Among carnivores, competition is particularly
 pronounced with the strongest interactions between similar species with
 intermediate differences in body size. While ecologists have emphasized
 interference competition among carnivores based on dominance hierarchies
 from body size (smaller = subordinate; larger = dominant), the reciprocity
 of exploitative competition from subordinate species has been overlooked
 even though efficient exploitation can limit resource availability and
 influence foraging. Across North America, fishers (Pekania pennanti) and
 martens (Martes spp.) are two phylogenetically related forest carnivores
 that exhibit a high degree of overlap in habitat use and diet and differ
 in body size by a factor of 2–5x, eliciting particularly strong
 interspecific competition. In the Great Lakes region, fishers and martens
 occur both allopatrically and sympatrically; where they co-occur, the
 numerically dominant species varies spatially. This natural variation in
 competitors and environmental conditions enables comparisons to understand
 how interference and exploitative competition alter dietary niche overlap
 and foraging strategies. We analyzed stable isotopes (δ13C and δ15N) from
 317 martens and 132 fishers, as well as dietary items (n = 629) from 20
 different genera, to compare niche size and overlap. We then quantified
 individual diet specialization and modeled the response to environmental
 conditions that were hypothesized to influence individual foraging.
 Martens and fishers exhibited high overlap in both available and core
 isotopic δ-space, but no overlap of core dietary proportions. When the
 competitor was absent or rare both martens and fishers consumed more
 smaller-bodied prey. Notably, the dominant fisher switched from being a
 specialist of larger to smaller prey in the absence of the subordinate
 marten. Environmental context also influenced dietary specialization:
 increasing land cover diversity and prey abundance reduced specialization
 in martens whereas vegetation productivity increased specialization for
 both martens and fishers. Despite an important dominance hierarchy,
 fishers adjusted their niche in the face of a subordinate, but superior,
 exploitative competitor. These findings highlight the underappreciated
 role of the subordinate competitor in shaping the dietary niche of a
 dominant competitor.
DOI: 10.5061/dryad.j6q573nkg
title: Host associated transmission favors transition of a commensal toward antagonism

description: The impacts of host-associated microbes for their hosts varies along a
 continuum of antagonistic, neutral, and beneficial interactions.
 Transmission mode is predicted to contribute to transitions along the
 continuum by altering opportunities for the alignment of host and microbe
 fitness interests.  Under vertical transmission, microbial
 evolution is tightly coupled to the host environment, which may facilitate
 fitness alignment. In contrast, environmentally transmitted microbes spend
 time in the external environment, outside of hosts, partially decoupling
 their evolution from the host. This decoupling may misalign host and
 microbe fitness interests, potentially favoring antagonistic microbial
 traits. Here, we tested whether transmission environment alters microbial
 evolution by manipulating the interaction between a commensal Serratia
 marcescens bacteria and their insect host Anasa tristis, which are the
 primary vector of these bacteria into plants, where they cause disease. We
 experimentally evolved S. marcescens through several selection
 environments. The bacteria were passaged between A. tristis hosts, between
 A. tristis hosts and soil, through soil, or through standard culture
 media. We observed rapid evolution of virulence toward hosts across
 treatments when bacterial evolution occurred within the host environment,
 indicating that direct host-to-host transmission can increase
 opportunities for microbes to adapt to hosts and evolve antagonistic
 traits.
DOI: 10.5061/dryad.m905qfv69
title: Dietary flavanols restore hippocampal-dependent memory in older adults with lower diet quality and habitual flavanol consumption

description: Dietary flavanols are food constituents found in certain fruits and
 vegetables that have been linked to cognitive aging. Previous studies
 suggested that consumption of dietary flavanols might specifically be
 linked to the hippocampal-dependent memory component of cognitive aging
 and that memory benefits of a flavanol intervention might depend on
 habitual diet quality. Here, we tested these hypotheses in the context of
 a large-scale study of 3,562 older adults, who were randomly assigned to a
 3-y intervention of cocoa extract (500 mg of cocoa flavanols per day) or a
 placebo [(COcoa Supplement and Multivitamin Outcomes Study) COSMOS-Web,
 NCT04582617]. Using the alternative healthy eating index in all
 participants and a urine-based biomarker of flavanol intake in a subset of
 participants [n = 1,361], we show that habitual flavanol consumption and
 diet quality at baseline are positively and selectively correlated with
 hippocampal-dependent memory. While the prespecified primary endpoint
 testing for an intervention-related improvement in memory in all
 participants after 1 y was not statistically significant, the flavanol
 intervention restored memory among participants in lower tertiles of
 habitual diet quality or habitual flavanol consumption. Increases in the
 flavanol biomarker over the course of the trial were associated with
 improving memory. Collectively, our results allow dietary flavanols to be
 considered in the context of a depletion–repletion paradigm and suggest
 that low flavanol consumption can act as a driver of the
 hippocampal-dependent component of cognitive aging.
description: SAS
DOI: 10.15468/dl.wce3sq
title: Occurrence Download

description: A dataset containing 55387 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Living Specimen)",
 "Continent is Europe",
 "TaxonKey is Ovis aries"
 ]
}

 The dataset includes 55387 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003000-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tht76hf4d
title: Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis

description: A set of newly designed Vitaceae baits targeting 1013 genes was employed
 to explore phylogenetic relationships among North American Vitis.
 Eurasian Vitis taxa including Vitis vinifera were found to be
 nested within North American Vitis subgenus Vitis. North American Vitis
 subgenus Vitis can be placed into nine main groups: the Monticola
 group, the Occidentales group, the Californica group, the Vinifera group
 (introduced from Eurasia), the Mustangensis group, the Palmata group, the
 Aestivali group, the Labrusca group, and the Cinerea group.
 Strong cytonuclear discordances were detected in North American
 Vitis, with many species non-monophyletic in the plastid
 phylogeny, while monophyletic in the nuclear phylogeny. The
 phylogenomic analyses support recognizing four distinct species
 in the Vitis cinerea complex in North America: V. cinerea, V.
 baileyana, V. berlandieri, and V. simpsonii. Such treatment
 will better serve the conservation of wild Vitis diversity in
 North America.
DOI: 10.5061/dryad.nvx0k6dxm
title: Copepod life history evolution under high and low food regimes

description: Copepods play a critical role in the carbon cycle of the planet – they
 mediate the sequestration of carbon into the deep ocean, and are the
 trophic link between phytoplankton and marine foodwebs. Global change
 stressors that decrease copepod productivity create the potential for
 catastrophic positive feedback loops. Accordingly, a growing list of
 studies examine the evolutionary capacity of copepods to adapt to the two
 primary stressors associated with global change: warmer temperatures and
 lower pH. But the evolutionary capacity of copepods to adapt to changing
 food regimes, the third major stressor associated with global change,
 remains unknown. We used experimental evolution to explore how a 10-fold
 difference in food availability affects life history evolution in the
 copepod, Tisbe sp. over two years, and spanning 30+ generations. Different
 food regimes evoked evolutionary responses across the entire copepod life
 history: we observed evolution in body size, size-fecundity relationships,
 and offspring investment strategies. Our results suggest that changes to
 food regimes reshape life histories and that cryptic evolution in traits
 such as body size is likely. We demonstrate that evolution in response to
 changes in ocean productivity will alter consumer life histories, and may
 distort trophic links in marine foodchains. Evolution in response to
 changing phytoplankton productivity may alter the efficacy of the global
 carbon pump in ways that have not been anticipated until now.