cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j9kd51c8j
title: Perturbation drives changing metapopulation dynamics in a top marine predator

description: Metapopulation theory assumes a balance between local decays/extinctions
 and local growth/new colonisations. Here we investigate whether recent
 population declines across part of the UK harbour seal range represent
 normal metapopulation dynamics or are indicative of perturbations
 potentially threatening the metapopulation viability, using 20 years of
 population trends, location tracking data ( n = 380), and UK-wide,
 multi-generational population genetic data ( n = 269). First, we use
 microsatellite data to show that two genetic groups previously identified
 are distinct metapopulations: northern and southern. Then, we characterize
 the northern metapopulation dynamics in two different periods, before and
 after the start of regional declines (pre-/peri-perturbation). We identify
 source–sink dynamics across the northern metapopulation, with two putative
 source populations apparently supporting three likely sink populations,
 and a recent metapopulation-wide disruption of migration coincident with
 the perturbation. The northern metapopulation appears to be in decay,
 highlighting that changes in local populations can lead to radical
 alterations in the overall metapopulation's persistence and dynamics.
description: See manuscript
description: This archive contains two files
 1. Genelemetry_harbour_seal_metadata_dryad_final.xlsx
 Excel file containing metadata for samples used in the paper
 analysis, including sampling location, sampling seal management unit, and
 local population
 2. HarbourSealGenepopFormat.txt Text file
 containing multi-locus genotypes for harbour seals used in the analysis in
 genepop format.
DOI: 10.5066/p13bb4rx
title: Lake Erie hydroacoustic vessel comparison data: research vessels vs. uncrewed surface vessel

description: This dataset is from a vessel comparison study between four motorized research vessels (RVs) and one uncrewed surface vessel (USV) including the Ohio Department of Natural Resources (ODNR) RV Almar and RV Grandon, the U.S. Geological Survey (USGS) RV Muskie, the Ontario Ministry of Natural Resources (OMNR) RV Erie Explorer and a wind propelled USV (SD-1080; Saildrone Inc.). Paired acoustic data were collected along 2-km transects during five sampling events distributed across the U.S. waters of Lake Erie. Additional information related to environmental conditions and vessel stability was also collected. Data were used to compare and explain variations in acoustic measurements between RVs and the USV.
DOI: 10.5061/dryad.t1g1jwt02
title: Data from: Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii

description: Different host species often differ considerably in susceptibility to a
 given pathogen, but the causes of such differences are rarely known. The
 natural hosts of the tick-transmitted bacterium Borrelia afzelii,
 which is one of causative agents of Lyme borreliosis in
 humans, include a variety of small mammals like voles and mice. Previous
 studies have shown that B. afzelii-infected bank voles (Myodes
 glareolus) have about ten times higher bacterial load than infected
 yellow-necked mice (Apodemus flavicollis), indicating that these two
 species differ in resistance. In this study, we compared the immune
 response to B. afzelii infection in these host species
 by using RNA-sequencing to quantify gene expression in spleen. Gene set
 enrichment analysis (GSEA) showed that several immune pathways were
 down-regulated in infected animals in both bank voles and yellow-necked
 mice. Moreover, IFNα response was up-regulated in B.
 afzelii-infected yellow-necked mice, while IL6 signaling and the
 complement pathway were down-regulated in infected bank voles; differences
 in regulation of these three pathways between bank voles and yellow-necked
 mice could thus contribute to the difference in resistance to B.
 afzelii between the species. This study provides knowledge of
 gene expression induced by a zoonotic pathogen in its natural host, and
 possible species-specific regulation of immune responses associated with
 resistance.
description: <strong>bv_annotated_de_novo_transcriptome.fasta</strong> Fasta file contains annotated de novo assembled contigs from bank vole. <strong>ynm_annotated_de_novo_transcriptome.fasta</strong> Fasta file contains annotated de novo assembled contigs from yellow-necked mouse. <strong>bv_counts_matrix</strong> Counts of each annotated gene used for differential expression in bank vole. <strong>ynm_counts_matrix</strong> Counts of each annotated gene used for differential expression in yellow-necked mouse.
DOI: 10.5061/dryad.s1rn8pk4v
title: Plant traits, biotopes and urbanization dynamics explain the survival of endangered urban plant populations

description: 1. With accelerating urbanization, the urban contribution to biodiversity
 conservation becomes increasingly important. Previous research shows that
 cities can host many endangered plant species. However, fundamental
 questions for urban nature conservation remain open: to what extent and
 where can endangered plant species persist in the long term and which
 mechanisms underlie population survival? 2. We evaluate the survival of
 858 precisely monitored populations of 179 endangered plant species in
 Berlin, Germany, by assessing population survival throughout different
 urban ecosystems over a period of 7.6 years on average. By linking
 population survival to various landscape variables and plant traits, we
 unravel the underlying drivers. 3. More than one third of populations went
 extinct during the observation period. Population survival was inversely
 correlated to the increase of impervious surfaces in the vicinity
 following the first 11 years after the fall of the Berlin wall.
 Additionally, populations in semi-natural habitats like forests and bogs
 were surprisingly more prone to local extinction than populations in
 anthropogenic habitats. Survival was highest for competitive species with
 a preference for drier soils (Ellenberg indicator for soil humidity). 4.
 Synthesis and applications. Considerable levels of local population
 extinction demonstrate that the presence of endangered plants cannot be
 directly linked with their long-term survival in cities. However the
 survival of remaining populations indicates opportunities for urban
 biodiversity conservation both within and outside conservation areas. The
 elucidated links between population survival, urbanization dynamics,
 biotope class, and species traits support urban conservation strategies
 that reduce the proportion of impervious surface, prioritize conservation
 management in forests and grasslands and explore the opportunities of
 green spaces and built up areas.
description: The population monitoring data was provided by Justus Meißner and
 the Stiftung Naturschutz Berlin, as part of their Berliner
 Florenschutzkonzept programme. The biotope and urbanisation data was
 provided by Berlin’s Senate Department of Urban Development and
 Environment, as part of the Berlin Environmental Atlas and the Berlin
 Social Urban Development Monitoring. Data on plaint traits was gathered
 from the BIOFLOR database.
description: For information about the units used for each variable, and how
 each variable was used in the statistical models, please consult the
 Appendix of the original publication.
DOI: 10.5061/dryad.8kprr4xk3
title: Supplemental materials for: Peri- and post-pubertal estrogen exposures of female mice optimize uterine responses later in life

description: At birth, all female mice, including those that either lack estrogen
 receptor α (ERα-knockout) or that express mutated forms of ERα (AF2ERKI),
 have a hypoplastic uterus. However, uterine growth and development that
 normally accompanies pubertal maturation does not occur in ERα-knockout or
 AF2ERKI mice, indicating ERα mediated estrogen signaling is essential for
 this process. Mice that lack Cyp19 (aromatase, ArKO mice), an enzyme
 critical for estrogen (E2) synthesis, are unable to make E2, and lack
 pubertal uterine development. A single injection of E2 into ovariectomized
 adult (10 weeks old) females normally results in uterine epithelial cell
 proliferation, however, we observe that, although ERα is present in the
 ArKO uterine cells, no proliferative response is seen. We assessed the
 impact of exposing ArKO mice to E2 during pubertal and post-pubertal
 windows and observed that E2 exposed ArKO mice acquired growth
 responsiveness. Analysis of differential gene expression between unexposed
 ArKO samples and samples from animals exhibiting the ability to mount an
 E2-induced uterine growth response (WT or E2 exposed ArKO) revealed
 activation of EZH2 and HAND2 signaling and inhibition of GLI1 responses.
 EZH2 and HAND2 are known inhibit uterine growth, and GLI1 is involved in
 IHH signaling, which is a positive mediator of uterine response. Finally,
 we show that exposure of ArKO females to dietary phytoestrogens results in
 their acquisition of uterine growth competence. Altogether our findings
 suggest that pubertal levels of endogenous and exogenous estrogens impact
 biological function of uterine cells later in life via ERα-dependent
 mechanisms.
DOI: 10.5061/dryad.bnzs7h478
title: Data from: Tree seedling responses to leaf-cutting ants herbivory in Atlantic Forest restoration sites

description: Leaf-cutting ants (LCA) are generalist herbivores capable of causing
 severe plant damage. Negative impacts of ant herbivory vary according to
 the density of nests and availability of palatable plants; however, it is
 not yet clear how these herbivores affect tropical forest restoration
 sites. To investigate how LCA preference affects plant species
 performance, we evaluated the herbivory of Atta sexdens rubropilosa on
 native tree species seedlings in Atlantic Forest restoration sites. We
 expected pioneer species to suffer higher herbivory by LCA when compared
 with non-pioneer species, and that species with higher damage will have
 poorer growth and higher mortality. The experiment was conducted in three
 restoration sites in northern Paraná state, southern Brazil, with 1500
 seedlings of 5 pioneer and 5 non-pioneer species. Sites share similar age,
 stand size, tree species composition, and LCA nest density. The number of
 attacks, degree of leaf damage, number of leaves, plant height and
 survival were recorded. Specific leaf area, leaf polyphenols, flavonoids,
 tannins, and nitrogen content were analyzed for each species. Plant damage
 was similar between pioneer and non-pioneer plant species. This could be
 explained by trait variability among species in each group and by LCA
 generalist foraging. Preferred species suffered decreases in growth and
 survival. Less preferred species suffered fewer ant attacks and no change
 in performance. Results suggest that ant herbivory can influence plant
 species establishment and thus species composition in restoration sites by
 reducing performance and increasing mortality of some, but not all
 species, making LCA an important ecological filter.
description: The dataset presents the raw data transferred from field
 notebooks, except for variables were calculations were  added (IH and
 RGR). No further processing was done. Metadata were included in the
 spreadsheed, but do not hesitate in contact us.
DOI: 10.5061/dryad.547d7wm5h
title: Data from: The beautiful and the dammed: defining multi-stressor disturbance regimes in an Atlantic river floodplain wetland

description: Natural hydrological fluctuations within river floodplains generate
 habitat diversity through variable connections between habitat patches and
 the main river channel. Human modification of floodplains can alter the
 magnitude and frequency of large floods and associated sediment movement
 by interrupting these floodplain connections. The lower Wolastoq | Saint
 John River and its associated floodplain wetlands are experiencing
 anthropogenic disturbances arising from climate change, increased
 urbanization in the watershed, changing upstream agricultural landscape
 practices, and, most notably, major road and dam construction. By
 comparing digitized aerial images, we identified key periods of change in
 wetland extent throughout an ecologically significant component of the
 floodplain, the Grand Lake Meadows and Portobello Creek wetland complex,
 with significant erosion evident in coves and backwater areas across the
 landscape following dam construction and significant accretion around the
 Jemseg River following highway construction. Connectivity and hydrological
 regime also influenced other habitat components, namely nutrients and
 metals retention, as well as the composition of the local macrophyte
 community. These findings address two key aspects of floodplain
 management: (1) understanding how hydrological alteration has historically
 influenced floodplain wetlands can inform us of how the ecosystem may
 respond under future conditions, such as climate change, and (2) the
 mechanisms by which habitat diversity and disturbance regimes filter
 biological communities, with the potential for patches to host a rich
 biodiversity continuously supporting critical ecosystem functions.
description: See paper for detailed description.
description: Dataset associated with:  Rideout, N.K.,
 Compson, Z.G., Monk, W.A., Bruce, M.R. and Baird, D.J. (2021). The
 beautiful and the dammed: Defining multi-stressor disturbance regimes in
 an Atlantic river floodplain. <em>Frontiers in Ecology and
 Evolution. </em>https://doi.org/10.3389/fevo.2021.553094
DOI: 10.5066/p14bqgbg
title: Decision model simulation of the reintroduction of bull trout in the upper Lake Chelan basin, Washington

description: The feasibility of a potential bull trout (Salvelinus confluentus) reintroduction was simulated across 12 streams and river segments in the upper Lake Chelan basin using a population matrix model. The model considered habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Details of the simulation framework are described in Benjamin et al., 2024 (submitted publication). Scenarios for model simulations included life stage, number of individuals, and years following potential reintroduction. We considered, four life stages of bull trout, eggs, juveniles, subadults and adults. Each life stage has three options for the numbers of individuals reintroduced. For eggs, it was the addition of 5,000, 10,000 and 20,000 individuals; for juveniles, 200, 500, and 2000 individuals; and for subadults and adults, 30, 60 and 100 individuals. Simulated numbers of adult bull trout are provided over 5 time periods (5,10, 30, 50 and 70 years after reintroduction). Here, in the data tables, we provide results from a one-way sensitivity analyses and global sensitivity analyses as well as the potential effect of dispersal on simulated bull trout populations.
DOI: 10.5061/dryad.xwdbrv1b3
title: Data from: Trophic niche size and overlap decreases with increasing ecosystem productivity

description: The production and transfer of biomass through trophic relationships is a
 core ecosystem function. The movement of energy through the food web is
 mediated by organisms operating in their niche space. For generalists, the
 size of this niche space is inherently plastic and changes in response to
 available food sources. Therefore, this relationship between ecosystem
 productivity and niche size is an important determinant of ecosystem
 function. Competing theories about the nature of this relationship predict
 that as productivity increases niche size will either increase as species
 capitalize on a general increase in resource availability or decrease as
 it becomes viable to focus on preferred production channels. Here, we test
 these two competing theoretical frameworks using a novel approach to
 determine trophic niche size using stable isotope analysis and hypervolume
 metrics. Resource use is quantified in two generalist fish species at
 three productivity levels in a seagrass ecosystem. Niche size of both
 species was inversely related to seagrass productivity, consistent with
 the hypothesis that increasing productivity allows species to focus on a
 narrower diet. This pattern describes the relationship between ecosystem
 production and niche size and provides an empirical ecological explanation
 for the resource maximization behaviors commonly observed in nature.
description: R code is set up to run with included isotope data.
DOI: 10.5061/dryad.98sf7m0fv
title: Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

description: Background: Tracing the association between insect cold tolerance and
 latitudinally and locally varying environmental conditions, as well as key
 morphological traits and molecular mechanisms, is essential for
 understanding the processes involved in adaptation. We explored these
 issues in two closely-related species, Drosophila montana and Drosophila
 flavomontana, originating from diverse climatic locations across several
 latitudes on the coastal and mountainous regions of North America. We also
 investigated the association between sequence variation in one of the key
 circadian clock genes, vrille, and cold tolerance in both species.
 Finally, we studied the impact of vrille on fly cold tolerance and cold
 acclimation ability by silencing it with RNA interference in D. montana.
 Results: We performed a principal component analysis (PCA) on variables
 representing bioclimatic conditions on the study sites and used latitude
 as a proxy of photoperiod. PC1 separated the mountainous continental sites
 from the coastal ones based on temperature variability and precipitation,
 while PC2 arranged the sites based on summer and annual mean temperatures.
 Cold tolerance tests showed D. montana to be more cold-tolerant than D.
 flavomontana and chill coma resistance (CTmin) of this species showed an
 association with PC2. Chill coma recovery time (CCRT) of both species
 improved towards northern latitudes, and in D. flavomontana this trait was
 also associated with PC1. D. flavomontana flies were darkest in the coast
 and in the northern mountainous populations, but coloration showed no
 linkage with cold tolerance. Body size decreased towards cold environments
 in both species, but only within D. montana populations largest flies
 showed fastest recovery from cold. Finally, both the sequence analysis and
 RNAi study on vrille suggested this gene to play an essential role in D.
 montana cold resistance and acclimation, but not in recovery time.
 Conclusions: Our study demonstrates the complexity of insect cold
 tolerance and emphasizes the need to trace its association with multiple
 environmental variables and morphological traits to identify potential
 agents of natural selection. It also shows that a circadian clock gene
 vrille is essential both for short- and long-term cold acclimation,
 potentially elucidating the connection between circadian clock system and
 cold tolerance.
DOI: 10.5061/dryad.cfxpnvx30
title: Data from: The Collins’ monster, a spinous suspension-feeding lobopodian from the Cambrian Burgess Shale of British Columbia

description: Lobopodians, a paraphyletic group of Palaeozoic vermiform animals bearing
 metameric appendages, are key to the origin of extant panarthropods. First
 discovered in 1983 on Mount Stephen (Yoho National Park, British
 Columbia), the Cambrian (Wuliuan) Burgess Shale lobopodian nicknamed
 “Collins’ monster” is formally described as Collinsovermis monstruosus
 gen. et sp. nov. A formal systematic revision of the poorly known
 lobopodian Acinocricus stichus from Utah is also provided. The body of
 Collinsovermis is plump and compact, lacking space between lobopod pairs
 but shows the diagnostic suspension-feeding characters of luolishaniid
 lobopodians. The six anterior lobopod pairs are elongate, adorned with
 long and slightly curved ventral spinules arranged in a chevron-like
 pattern. The eight posterior lobopod pairs, which attach to a truncated
 body termination, are stout and smooth, each terminated by a single strong
 recurved claw. Each somite bears a pair of dorsal spines; somites 4 and
 posteriad bear an additional median spine. The spines on somites 1–3 are
 much shorter than the spines on the remaining somites. The head is short,
 bears a pair of antenniform outgrowths, and is covered by an oblong
 sclerite. Collinsovermis plus Collinsium and Acinocricus comprise a
 sub-group of stout luolishaniid lobopodians with remarkably long spinules
 on the front lobopods, interpreted here as a clade (Teratopodidae). This
 clade is distinct from both the comparatively slenderer Luolishania and a
 sub-group composed of Facivermis and Ovatiovermis with posterior lobopods
 reduced or absent. Luolishaniids were mostly sessile forerunners of
 arthropods that had coupled efficient suspension-feeding devices and, as
 in Collinsovermis defensive features.
description: The phylogenetic analysis was primarily based on morphological
 observations of fossil specimens.
DOI: 10.5281/zenodo.17993437
title: Open Datasets for Manuscript entitled "Toward Efficient Resource Adequacy: The Role of Shared Reserves in China's Power Grid" in Energy Strategy Reviews

description: This collection contains datasets for the manuscript “Toward Efficient Resource Adequacy: The Role of Shared Reserves in China’s Power Grid” in Energy Strategy Reviews, including input files for Gridpath V0.10.0 for the capacity expansion and production cost analysis by considering the planning and operating reserves sharing strategies.  The input_v10.zip contains the capacity expansion input files for Gridpath, and PC_input.zip contains the production cost input files.
DOI: 10.5281/zenodo.17993436
title: Open Datasets for Manuscript entitled "Toward Efficient Resource Adequacy: The Role of Shared Reserves in China's Power Grid" in Energy Strategy Reviews

description: This collection contains datasets for the manuscript “Toward Efficient Resource Adequacy: The Role of Shared Reserves in China’s Power Grid” in Energy Strategy Reviews, including input files for Gridpath V0.10.0 for the capacity expansion and production cost analysis by considering the planning and operating reserves sharing strategies.  The input_v10.zip contains the capacity expansion input files for Gridpath, and PC_input.zip contains the production cost input files.