cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bzkh1899m
title: Seasonal variation of population and individual dietary niche in the avivorous bat, Ia io

description: The variation in niche breadth can affect how species respond to
 environmental and resource changes. However, there is still no clear
 understanding of how seasonal variability in food resources impacts the
 variation of individual dietary diversity, thereby affecting the dynamics
 of a population’s dietary niche breadth. Optimal foraging theory (OFT) and
 the niche variation hypothesis (NVH) predict that when food resources are
 limited, the population niche breadth will widen or narrow due to
 increased within-individual dietary diversity and individual
 specialization or reduced within-individual dietary diversity,
 respectively. Here, we used DNA metabarcoding to examine the composition
 and seasonality of diets of the avivorous bat Ia io. Furthermore, we
 investigated how the dietary niches changed among seasons and how the
 population niche breadth changed when the availability of insect resources
 was reduced in autumn. We found that there was differentiation in dietary
 niches among seasons and a low degree of overlap, and the decrease of
 insect resource availability and the emergence of ecological opportunities
 of nocturnal migratory birds might drive dietary niche shifts toward birds
 in I. io. However, the population’s dietary niche breadth did not broaden
 by increasing the within-individual dietary diversity or individual
 specialization but rather became narrower by reducing dietary diversity
 via predation on bird resources that served as an ecological opportunity
 when insect resources were scarce in autumn. Our findings were consistent
 with the predictions of OFT because birds as prey for bats provided
 extremely different resources from those of insects in size and
 nutritional value. Our work highlights the importance of size and quality
 of prey resources along with other factors (i.e., physiological,
 behavioral, and life-history traits) in dietary niche variation.
description: Refer to the README for description of included data files.
DOI: 10.5061/dryad.fxpnvx0sm
title: Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

description: Interspecific gene flow by hybridization may weaken species barriers and
 adaptive divergence, but can also initiate reinforcement of reproductive
 isolation through natural and sexual selection. However, the extent of
 interspecific gene flow and its consequences for the initiation and
 maintenance of species barriers in natural systems remain poorly
 understood. We first applied coalescence simulations and approximate
 Bayesian calculations based on microsatellite data to infer the yet
 unknown demographic history of the two closely related European dung fly
 sister species Sepsis cynipsea and Sepsis neocynipsea (Diptera: Sepsidae).
 To assess genome-wide patterns of historical gene flow between both
 species, we quantified discordances in derived allele sharing
 (D-statistics, ABBA-BABA test) in whole-genome resequencing data from
 pooled DNA of male specimens originating from natural and laboratory
 populations. We contrasted genome-wide variation in DNA sequence
 differences between samples from sympatric populations of the two species
 in France and Switzerland with that of interspecific differences between
 pairs of samples involving allopatric populations from Estonia and Italy.
 At one site in the French Cevennes we detected a relative excess of DNA
 sequence identity, suggesting interspecific gene flow in sympatry. In
 contrast, at two sites in Switzerland, we observed a relative depletion of
 DNA sequence identity compatible with reinforcement of species boundaries
 in sympatry. Our results suggest that the species boundaries between S.
 cynipsea and S. neocynipsea in Europe depend on the eco-geographic
 context.
description: Two dimensional matrix of allele frequencies for genome-wide SNPs
 (rows) and population samples (columns)
DOI: 10.5281/zenodo.18396677
title: Jicamarca-Piura Magnetometer DeltaH Climatology
DOI: 10.5281/zenodo.18396676
title: Jicamarca-Piura Magnetometer DeltaH Climatology
DOI: 10.5061/dryad.pk0p2ngpj
title: Bizarre tail weaponry in a transitional ankylosaur from subantarctic Chile

description: Armoured dinosaurs are well known for their evolution of specialized tail
 weapons— paired tail spikes in stegosaurs and heavy tail clubs in advanced
 ankylosaurs1. Armoured dinosaurs from southern Gondwana are rare and
 enigmatic, but probably include the earliest branches of Ankylosauria2–4.
 Here we describe a mostly complete, semi-articulated skeleton of a small
 (approximately 2 m) armoured dinosaur from the late Cretaceous period of
 Magallanes in southernmost Chile, a region that is biogeographically
 related to West Antarctica5. Stegouros elengassen gen. et sp. nov. evolved
 a large tail weapon unlike any dinosaur: a flat, frond-like structure
 formed by seven pairs of laterally projecting osteoderms encasing the
 distal half of the tail. Stegouros shows ankylosaurian cranial characters,
 but a largely ancestral postcranial skeleton, with some stegosaur-like
 characters. Phylogenetic analyses placed Stegouros in Ankylosauria;
 specifically, it is related to Kunbarrasaurus from Australia6 and
 Antarctopelta from Antarctica7, forming a clade of Gondwanan ankylosaurs
 that split earliest from all other ankylosaurs. The large osteoderms and
 specialized tail vertebrae in Antarctopelta suggest that it had a tail
 weapon similar to Stegouros. We propose a new clade, the Parankylosauria,
 to include the first ancestor of Stegouros— but not Ankylosaurus—and all
 descendants of that ancestor.
DOI: 10.5061/dryad.mw6m905xg
title: RNA sequencing of PET127 mutants overexpressed using the galactose inducible promoter

description: In Saccharomyces cerevisiae, PET127 is a mitochondrial RNA exonuclease
 known to interact with the mitochondrial RNA polymerase RPO41. The nature
 of the interaction between PET127 and RPO41 is
 unclear. Here, we overexpressed different PET127 mutants for five
 hours utilizing the galactose inducible promoter on high-copy
 plasmids, collected samples, and performed RNA sequencing to
 understand the mitochondrial RNA landscape in each condition. The mutants
 tested were PET127 lacking the nuclease activity
 (pet127-nd) and two truncated forms of PET127: either lacking
 the RPO41 binding region (pet127∆(48-215)), or only
 containing the RPO41 binding region (pet127(1-215)).
description: RNA was isolated from 4.4 x 107 cells of cells using acid phenol
 and purified using RNeasy kit (Qiagen) with on column DNAse treatment
 (Qiagen). Isolated total yeast RNA were processed using Ribozero rRNA
 removal for Yeast (Illumina). Samples were collected upon
 addition of galactose and 5 hours after the addition of
 galactose. Sequencing was performed on HiSeq2000 with 40
 bases single end run with 8 + 8 nucleotide indexes.
DOI: 10.5061/dryad.0gb5mkm23
title: GIbase 1.0 Green Infrastructure plant species in England and Scotland

description: 1. The contributions of constructed Green Infrastructure (GI) to
 biodiversity are often used to justify urban development projects, yet in
 many cases these contributions have been difficult to quantify. 
 2. As a result, a wide range of GI features are designed and implemented,
 often without knowledge of whether these features contribute meaningfully
 to biodiversity or if there are biosecurity risks presented by their
 design or procurement. Our understanding of design practices could be
 significantly improved if researchers and policy makers were able to draw
 upon a data resource that recorded the specifications used in development
 projects and facilitated easy access to them.  3. In the UK,
 Planning Portals act as substantial and untapped repositories of grey
 literature, containing highly detailed data with a diverse spatial
 coverage, recording the diversity and extent of existing habitats and
 specifications for proposed species assemblages. However, they are
 difficult to navigate or query, making it challenging to use these
 resources to gain macro-level insights from the data held within the
 portals.  4. In this paper, we present Plant GI 1.0, a new
 dataset that incorporates plant specifications from development projects
 across England and Scotland along with trait data associated with each
 species. 5. To test whether these data could be used to inform policy
 makers and researchers about current procurement and planting practices,
 we assessed the proposed GI features that are submitted by developers to
 Local Planning Authorities as part of the planning process, and then
 carried out fieldwork to record the extent to which these specifications
 were delivered. 
description: Green infrastructure design specifications for urban development
 projects in England and Scotland were accessed through UK planning
 portals, and data were transcribed. Leaf functional traits were then
 derived for each species from TRY database, and CSR ordinations for each
 species were calculated using the StrateFy tool developed by Pierce et
 al., 2017.
DOI: 10.5061/dryad.66t1g1k2z
title: Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone

description: Hybridization can serve as an evolutionary stimulus, but we have little
 understanding of introgression at early stages of hybrid zone formation.
 We analyze reproductive isolation and introgression between a
 range-limited and a widespread species. Reproductive barriers are
 estimated based on differences in flowering time, ecogeographic
 distributions, and seed set from crosses. We find an asymmetrical mating
 barrier due to cytonuclear incompatibility that is consistent with
 observed clusters of coincident and concordant tension zone clines
 (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of
 concordant clines are spread across the hybrid zone, resulting in weak
 coupling among barrier loci and extensive introgression. Neutral clines
 had nearly equal introgression into both species’ ranges, while putative
 cases of adaptive introgression had exceptionally wide clines with centers
 shifted towards one species. Analyses of cline shape indicate that
 secondary contact was initiated within the last 800 generations with the
 per-generation dispersal between 200 and 400 meters, and provide some of
 the first estimates of the strength of selection required to account for
 observed levels of adaptive introgression. The weak species boundary
 between these species appears to be in early stages of dissolution, and
 ultimately will precipitate genetic swamping of the range-limited species.
description: Greenhouse crosses, seed counts, germination, flowering
 data.  GPSoccurances and bioclimatic data for
 environmental niche modeling. Herbarium records for
 phenology/flowering overlap. Genotyping by Sequencing
 SNP data analyzed for cline width and center.  Data
 Files Morphology. Petals (Petal
 Datcsv) Leaves (Leaf trichome data.csv)
 Greenhouse crosses. Seed set
 (filled, aborted, unfertilized)
 (Ranunc_Greenhouse_SeedCounts.csv) Germination
 (Germination data.csv) Flowering (Greenhouse
 flowering data.csv) Field
 seed set. 
 Seed set (filled, aborted, unfertilized) (Field seed set
 datcsv) Reproductive
 isolation. 
 ENM occurrences bioclim data
 (Ranunc_enm_bioclime_datcsv) Herbarium records
 (Ranunc_Flowering.csv) 
 Genetic data SNPs (50) fitting cline models
 (SNP 50 loci fitting cline models.csv) Clines center
 and width (HZAR Output Summary.csv) 
 Readme file with data descriptions: 
description: Missing values in all datasets.
DOI: 10.15468/dl.k6bckw
title: Occurrence Download

description: A dataset containing 772 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Freshwater Lamprey Survey Data"
 ]
}

 The dataset includes 772 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002941-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dz08kprzb
title: Of wolves and bears: Seasonal drivers of interference and exploitation competition between apex predators

description: Competition between apex predators can alter the strength of top-down
 forcing, yet we know little about the behavioral mechanisms that drive
 competition in multipredator ecosystems. Interactions between predators
 can be synergistic (facilitative) or antagonistic (inhibitive), both of
 which are widespread in nature, vary in strength between species and
 across space and time, and affect predation patterns and predator-prey
 dynamics. Recent research suggests gray wolf (Canis lupus) kill rates
 decrease where they are sympatric with brown bears (Ursus arctos),
 however, the mechanisms behind this pattern remain unknown. We used data
 from two long-term research projects in Scandinavia (Europe) and
 Yellowstone National Park (North America) to test the role of interference
 and exploitation competition from bears on wolf predatory behavior, where
 altered wolf handling and search time of prey in the presence of bears are
 indicative of interference and exploitation competition, respectively. Our
 results suggest the mechanisms driving competition between bears and
 wolves were dependent on the season and study system. During spring in
 Scandinavia, interference competition was the primary mechanism driving
 decreased kill rates for wolves sympatric with bears; handling time
 increased, but search time did not. In summer, however, when both bear and
 wolf predation focused on neonate moose, the behavioral mechanism switched
 to exploitation competition; search time increased, but handling time did
 not. Interference competition, however, did affect wolf predation dynamics
 in Yellowstone during summer, where wolves prey more evenly on neonate and
 adult ungulates. Here, bear presence at a carcass increased the amount of
 time wolves spent at carcasses of all sizes and wolf handling time for
 small prey, but decreased handling time for the largest prey. Wolves
 facilitate scavenging opportunities for bears, however, bears alter wolf
 predatory behavior via multiple pathways and are primarily antagonistic to
 wolves. Our study helps clarify the behavioral mechanisms driving
 competition between apex predators, illustrating how interspecific
 interactions can manifest into population-level predation patterns.
description: This data set was collected by two long-term research projects in
 Scandinavia and Yellowstone National Park. This data was cleaned and
 processes for a manuscript accepted into Ecological Monographs. 
description: The readme file contains an explanation of each of the variables
 in the dataset and their measurement units. Please see the full write-up
 in the Ecological Monographs article for the methods on dataset collection
 and processing.
DOI: 10.34808/f9rk-fa72
title: Effect of cavitation pretreatment on lactic acid production from food waste

description: Food waste (FW) fermentation to lactic acid (LA) represents a promising pathway for circular-economy valorisation. This study examined the use of low-frequency acoustic cavitation as a pretreatment strategy to improve FW solubilisation and enhance LA production under different substrate loadings, using two commonly applied anaerobic inocula. Cavitation substantially increased soluble organic matter availability and promoted LA formation, with higher substrate loadings generally leading to higher LA concentrations.
DOI: 10.5061/dryad.w3r2280rm
title: Memory array locations, delay times, and participant response

description: Deliberative decisions based on an accumulation of evidence over time
 depend on working-memory, and working memory has limitations, but how
 these limitations affect deliberative decision-making is not
 understood.  We used human psychophysics to assess the impact of
 working-memory limitations on the fidelity of a continuous decision
 variable.  Participants decided the average location of multiple
 visual targets.  This computed, continuous decision variable
 degraded with time and capacity in a manner that depended critically on
 the strategy used to form the decision variable.   This
 dependence reflected whether the decision variable was computed either: 1)
 immediately upon observing the evidence, and thus stored as a single value
 in memory; or 2) at the time of the report, and thus stored as multiple
 values in memory.  These results provide important constraints on
 how the brain computes and maintains temporally dynamic decision
 variables.  The following data is the responses and
 trial information collected from each subject in each condition:
 Simultaneous Perceived,  Simultaneous Computed, Sequential
 Perceived, and Sequential Computed.
description: This data was collected on Pavlovia in several different
 sessions.  The sessions have been concatonated across subjects and
 identifying information has been removed.  
description: Processing code for this dataset can be found
 in https://github.com/TheGoldLab/Memory_Diffusion_Task.  Specifically, the
 file
 "<strong>MDT_Main_Analysis_and_Figures.m"</strong>
DOI: 10.5061/dryad.4xgxd259x
title: Differential equity in access to public and private coastal infrastructure in the Southeastern United States

description: Despite the ubiquity of coastal infrastructure, it is unclear what factors
 drive its placement, particularly for water access infrastructure (WAI)
 that facilitates entry to coastal ecosystems such as docks, piers, and
 boat landings. The placement of WAI has both ecological and social
 dimensions, and certain segments of coastal populations may have
 differential access to water. In this study, we employed an environmental
 justice framework to assess how public and private WAI in South Carolina,
 USA is distributed with respect to race and income. Using publicly
 available data from state agencies and the US Census Bureau, we mapped the
 distribution of these structures across the 301 km of the South Carolina
 coast. Using spatially explicit analyses with high resolution, we found
 that census block groups with lower income contain more public WAI, but
 racial composition has no effect. On the other hand, private docks showed
 the opposite trends, as the abundance of docks is significantly,
 positively correlated with census block groups that have greater
 percentages of White residents, while income has no effect. Under a
 “need-based” model of equity, we argue that WAI are not equitably
 distributed in South Carolina and constitute an environmental justice
 issue. We contend that the racially unequal distribution of docks is
 likely a consequence of the legacy of Black land loss, especially of
 waterfront property, throughout the coastal Southeast over the past
 half-century. Knowledge of racially inequitable distribution of WAI can
 guide public policy to rectify this imbalance and support advocacy
 organizations working to promote public water access.  Our work
 also points to the importance of considering race in ecological research,
 as the spatial distribution of coastal infrastructure both directly
 affects ecosystems through the structures themselves and regulates which
 groups access water and what activities they can engage in at those sites.
description: Data was collected from state agencies in South Carolina and the
 American Community Survey. All analyses were conducted in ArcMap 10.6.1
 and R Version 4.0.4. A complete methodology can be found in the
 "Infrastructure Protocols and Guide.docx" file
 included.
description: R and ArcMap (10.6.X) or greater or ArcGIS Pro are required.
 There are no restrictions on usage, but it is suggested that users give
 credit to the original data source as well (South Carolina Department of
 Health and Environmental Control, Ocean and Coastal Resource Management
 Division).
DOI: 10.5061/dryad.bzkh1899p
title: Coastal uplift in the Kuroshio

description: The Kuroshio is the western boundary current of the North Pacific Ocean.
 In the subtropical region of eastern Taiwan, a coastal uplift of the
 isotherms has occurred. To explore its impact on this oligotrophic
 ecosystem, hydrographic data along the transect line at 23.75oN were
 measured between September 2012 and September 2014. Results show that the
 intensity of coastal uplift was positively correlated to the flow volume
 transport of the Kuroshio. Significant dissolved inorganic nutrients were
 uplifted to the sunlit zone, especially onshore. This dataset contains
 data collected from six shipboard measurements taken from the R/V Ocean
 Researcher I between September of 2012 and 2014: September and November
 2012, June and September 2013, and July and September 2014 in the
 Kuroshio, east of Taiwan described in the paper: “Chung-Chi Chen, Chun-Yi
 Lu, Sen Jan, Chih-Hao Hsieh, Chih-Ching Chung (2022). Effects of the
 coastal uplift on the Kuroshio ecosystem, eastern Taiwan, the western
 boundary current of the North Pacific Ocean. Frontiers in Marine Science“.
 The main results of this study included eight figures as described in the
 paper, and please refer to it for further details.
description: To understand the coastal uplift effect on the Kuroshio
 ecosystem, eight stations (K101–K108) along a transect (KTV1) between
 121.72° and 123°<sup> </sup>E at 23.75°<sup>
 </sup>N were repeatedly surveyed across the Kuroshio, east of
 Taiwan. At each station, seawater was sampled at eight depths (2–5, 10,
 30, 50, 100, 150, 200, and 250 m), using Teflon-coated Go-Flo bottles (20
 l, General Oceanics Inc., USA) mounted on a General Oceanic rosette
 assembly. Sub-samples were taken for analyses of dissolved inorganic
 nutrients (e.g., nitrate, phosphate, and silicate), chlorophyll
 <i>a</i> (Chl <i>a</i>), autotrophic picoplankton
 (e.g., <i>Synechococcus</i>,
 <i>Prochlorococcus</i>, and picoeukaryotes) and heterotrophic
 bacteria abundances. The analyzed methods for each variable can be found
 from the paper. The data has been processed by a linear regression
 analysis using “SigmaStat” to produce an ms accepted for publication in
 Frontiers in Marine Science.
description: The “README_coastal uplift” file contains an explanation of each
 of the variables in the dataset, its measurement units. Information on how
 the measurements were done or data were retrieved can be found in the
 associated manuscript referenced above.