cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wwpzgmsk4
title: Multiple-model stock assessment frameworks for precautionary management and conservation on fishery-targeted coastal dolphin populations off Japan

description: 1. Stock assessment approaches are often oversimplified due to lack of
 biological knowledge and insufficient data. In spite of worldwide
 attention, fishery-targeted coastal dolphin species in Japan have lacked
 in-depth quantitative stock assessments because of limited time-series of
 population size and an absence of associated biological information. We
 consequently developed integrated population models that analyzed multiple
 sources of data simultaneously with published biological information
 within a Bayesian framework. 2. We estimate population status and trends
 for three main species targeted by fisheries, bottlenose dolphins Tursiops
 truncatus, Risso’s dolphins Grampus griseus, and short-finned pilot whales
 Globicephala macrorhynchus, using single-species age-aggregated and
 age-structured population dynamics models. Models were fit to absolute
 abundance estimates from systematic line-transect surveys, four series of
 abundance indices calculated from fisher’s logbooks, and historical catch
 records. Published biological information was used to develop prior
 distributions for the biological parameters. We assessed the possible
 effects of ecological disturbance and competition using state-space and
 multispecies models. 3. The multispecies model was selected by the model
 selection both for the age-aggregated and the age-structured approaches.
 4. Single-species assessments found that population size declined 4.2%
 (Risso’s dolphin) to 8.0% (bottlenose dolphin) for three species since the
 late 1800s based on median posterior values, while the state-space and
 multispecies models found that environmental disturbance and an
 interaction among species could have reduced population size more
 substantially. 5. ‘Policy implications’ Simple single-species models are
 often used to provide conservation and management advice for wild animals
 but, in this case, results from such models are overly optimistic because
 they overlook important ecological process. In contrast, current
 population status could be less favorable if environmental disturbance and
 interspecific competition actually control population dynamics. Even if
 that is not the case, considering ecological process in the model will
 provide more precautionary ways. Our approach of combining multiple
 modelling frameworks is applicable to many other management systems, and
 offers increased confidence in estimated status and trends over
 assessments that consider only a single model.
description: All the methods are described in detail in the scientific paper
 associated.
description: See readme file for details.
DOI: 10.5061/dryad.wm37pvmn5
title: ANDEAN frugivory: data on plant–bird interactions and functional traits of plant and bird species from montane forests along the Andes

description: Species differ in their resource use and their interactions with other
 species and, consequently, they fulfil different functional roles in
 ecological processes. Species with specialized functional roles
 (specialists) are considered important for communities because they often
 interact with species with which few other species interact, thereby
 contributing complementary functional roles to ecological processes.
 However, the contribution of specialists could be low if they only
 interact with a small range of interaction partners. In contrast, species
 with unspecialized functional roles (generalists) often do not fulfil
 complementary roles but their contribution to ecological processes could
 be high because they interact with a large range of species. To
 investigate the importance of the functional roles of specialists versus
 generalists, we tested the relationship between species’ degree of
 specialization and their contribution to functional-role diversity for
 frugivorous birds in Andean seed-dispersal networks. We used two measures
 for the specialization of birds—one based on the size, and one based on
 the position of their interaction niche—and measured their effect on the
 birds’ contribution to functional-role diversity and their functional
 complementarity, a measure of how much a species’ functional role is
 complementary to those of the other species. In all networks, there were
 similar log-normal distributions of species’ contributions to
 functional-role diversity and functional complementarity. Contribution to
 functional-role diversity and functional complementarity increased with
 both increasing niche-position specialization and increasing niche size,
 indicating that the composition of functional roles in the networks was
 determined by an interplay between specialization and generalization.
 There was a negative interaction between niche-position specialization and
 niche size in both models, which showed that the positive effect of
 niche-position specialization on functional-role diversity and functional
 complementarity was stronger for species with a small niche size, and vice
 versa. Our results show that there is a continuum from specialized to
 generalized functional roles in species communities, and that both
 specialists and generalists fulfil important functional roles in
 ecological processes. Combining interaction networks with functional
 traits, as exemplified in this study, provides insight into the importance
 of an interplay of redundancy and complementarity in species’ functional
 roles for ecosystem functioning.
description: Data from:<br>Dehling DM, Bender IMA, Blendinger PG,
 Böhning-Gaese K, Muñoz MC, Neuschulz EL, Quitián M, Saavedra F, Santillán
 V, Schleuning M, Stouffer DB (2021) Specialists and generalists fulfil
 important and complementary functional roles in ecological processes.
 Functional Ecology, 35(8):1810–1821. doi:10.1111/1365-2435.13815
DOI: 10.5061/dryad.fj6q573v6
title: Stakeholders engagement as an important step for the long-term monitoring of wild ungulate populations

description: Monitoring trends in animal populations is essential for the development
 of appropriate wildlife management strategies. However, long-term studies
 are difficult to maintain mainly due to the lack of continuous funding. In
 this scenario, the collaboration between local stakeholders and
 researchers can be a fruitful partnership to monitor game species for long
 periods and vast territories. We present an experimental framework with
 the involvement of researchers, local hunters, and game managers for the
 continuous monitoring of wild ungulate populations. By combining
 vehicle-based counts with Distance sampling techniques, we implemented and
 validated a sampling scheme able to provide demographic information for
 the effective management of wild ungulate populations. Here, we used an
 Iberian red deer (Cervus elaphus) population as a model. The project
 implementation involved 30 participants including 24 stakeholders and 6
 field technicians/data analysts with experience in monitoring wild
 ungulates. A total of eight teams covered 29 itineraries, synchronously,
 in two periods of ecological relevance for red deer, early summer and
 early autumn. Density estimates were consistent among sampling periods and
 characterized by acceptable coefficients of variation (approximately 20%).
 Our results prove that the application of the proposed framework is
 feasible (3-4 itineraries per team), cost- and time-effective (one week
 per sampling period), and produce population estimates fit for management.
 Being based on direct observations, the method would provide important
 demographic indicators (e.g., population density, age structure and fawn
 recruitment, and group size) about wild ungulate populations. Apart from
 engaging interested stakeholders, the success of our proposal relies on
 three key actions including the theoretical and field instruction of
 participants, the definition of timely and unbiased survey designs, and
 the maintenance of participants’ motivation. The implementation of
 rigorous and standardized sampling protocols is pivotal for data
 integration through time and space. In the absence of continuous funding,
 the voluntary collaboration between entities should be fostered to study
 and mitigate the potential threats to wild ungulate populations resulting
 from disease, unregulated hunting, and environmental changes.
DOI: 10.5061/dryad.2fqz612p9
title: Data from: Opportunities for understanding MS mechanisms and progression with MRI using large‐scale data‐sharing and artificial intelligence

description: This is supplementary material accompanying the paper "Opportunities
 for understanding MS mechanisms and progression with MRI using large‐scale
 data‐sharing and artificial intelligence"
DOI: 10.5061/dryad.9zw3r22f6
title: Data for genetic characterization and curation of diploid a-genome wheat species

description: Diploid A-genome relatives of wheat comprises T. urartu, T. monococcum
 subsp. monococcum (domesticated einkorn) and T. monococcum subsp.
 aegilopoides (wild einkorn). About 930 accessions of A-genome diploid
 wheat species preserved in the gene bank of the Wheat Genetics Resource
 Center (WGRC) at Kansas State University were genotyped using
 genotyping-by-sequencing (GBS). We constructed four pooled GBS libraries
 (384- and 288-plex) using restriction enzymes (Pst1-Msp1) combinations and
 the libraries were sequenced on the Illumina platform. The sequence data
 was processed using Tassel 5 GBS v2 pipeline and identified thousands of
 single nucleotide polymorphisms (SNPs) for downstream genetic and genomic
 dissections of the tested population. We have used T. urartu
 pseudomolecule (Tu2.0) as a reference genome to detect the genetic
 markers. Four fastq files with raw sequence reads information can be
 obtained at the National Center for Biotechnology Information (NCBI) SRA
 database with the BioProject accession PRJNA744683
 (https://www.ncbi.nlm.nih.gov/sra/PRJNA744683). Provided key file has
 information for demultiplexing including flowcell, lane number, barcodes
 and sample names to replicate the analysis. This experiment led us to
 curate the gene bank through identification of genetically duplicated
 accessions, miss-classified accessions and miss-classified non-diploid
 accessions. We were able to observe the unique genetic and evolutionary
 relationships among the diploid A-genome wheat species along with the
 unique population structures per species and sub-species. 
description: The genotyping by sequencing (GBS) was performed  inorder to
 genotype wild wheat accessions. We obtained thousands of SNP markers from
 the sequencing work which was used to characterized the
 accessions.
DOI: 10.5061/dryad.4tmpg4f9r
title: Folding and unfolding of the tryptophan zipper in the presence of two thioamide substitutions

description: We studied the stability and folding and unfolding kinetics of the
 tryptophan zipper, containing dierent double thioamide subsitutions.
 Conformation change was triggered by photoisomerization of an integrated
 AMPP photoswitch in the turn region of the hairpin, and transient spectra
 were recorded in the deep UV and the mid-IR, covering the time window of
 the (un)folding transition from picoseconds to tens of microseconds.
 Thio-substitution of inward-pointing backbone carbonyls was found to
 strongly destabilize the β-hairpin structures, whereas molecules with two
 outward pointing thio-carbonyls showed similar or enhanced stability with
 respect to the unsubstituted sequence, which we attribute to stronger
 interstrand hydrogen bonding. Thiolation of the two Trp residues closest
 to the turn can even prevent the opening of the hairpin after cis-trans
 isomerization of the switch. The circular dichroism due to the two
 thioamide ππ∗ transitions is spectrally well-separated from the aromatic
 tryptophan signal. It changes upon photo-switching, reflecting a local
 change in coupling and geometry.
description: See methods section of the paper and supporting information.
description: ReadMe files describe the data structure organized by the figure
 number in the paper and the different sections of the SI. Data files can
 be associated by their name: filenames start with the figure number (or SI
 section), followed the experiment (trUV for transient UV, trIR for
 transient IR, sCD for static CD, UVvis for uv-visible absorption, MS for
 mass spectrum, NMR for nuclear magnetic resonance), date of acquisition
 and sample name. Further information at the end of the filename permits
 unique identification. Pdf files of mass spectra (SI section 2) contain
 explanations.
DOI: 10.5061/dryad.9p8cz8wgj
title: Data accessibility for conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

description: The quillwort Isoetes cangae is a critically endangered species occurring
 in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic
 diversity and small effective population sizes (Ne) is expected for narrow
 endemic species (NES). Here, we evaluated genetic diversity, population
 structure, and Ne of I. cangae to provide information for conservation
 programs. Conservation biology studies centered in a single‐species show
 some limitations but they are still useful considering the limited time
 and resources available for the protection of species at risk of
 extinction. Our analyses were based on 55 individuals collected from the
 Amendoim lake and 35,638 neutral SNPs. Our results indicated a single
 panmictic population, moderate levels of genetic diversity, and effective
 population size (Ne) in the order of thousands, contrasting the expected
 for NES. Negative FIS values were also found, suggesting that I. cangae is
 not under risk of inbreeding depression. Our findings imply that I. cangae
 contains enough genetic diversity to ensure evolutionary potential, all
 individuals should be treated as one demographic unit.
description: Here, we
 provide: - Draft genome for <i>Isoetes cangae</i>: and their raw data in .<strong>tar.gz </strong>and contigs alignment in <strong>.fasta</strong>. - R scripts for all analyses, and they are also available on: https://github.com/jdalapicolla/Isoetes_Scripts.R - Raw VCF and Filtered VCF files in .7z - Supplementary Information in .pdf
DOI: 10.5061/dryad.3r2280gg9
title: Cross-continental comparison of parasite communities in a wide-ranging carnivore suggests associations with prey diversity and host density

description: Parasites are integral to ecosystem functioning yet often overlooked.
 Improved understanding of host-parasite associations is important,
 particularly for wide-ranging species for which host range shifts and
 climate change could alter host-parasite interactions and their effects on
 ecosystem function. Among the most widely distributed mammals with diverse
 diets, grey wolves (Canis lupus) host parasites that are transmitted among
 canids and via prey species. Grey wolf-parasite associations may therefore
 influence the population dynamics and ecological functions of both wolves
 and their prey. Our goal was to identify large-scale processes that shape
 host-parasite interactions across populations, with the grey wolf as a
 model organism. By compiling data from various studies, we examined the
 faecal prevalence of gastrointestinal parasites in six wolf populations
 from two continents in relation to wolf density, diet diversity, and other
 ecological conditions. As expected, we found that the faecal prevalence of
 parasites transmitted directly to wolves via contact with other canids or
 their excreta was positively associated with wolf density. Contrary to our
 expectations, the faecal prevalence of parasites transmitted via prey was
 negatively associated with prey diversity. We also found that parasite
 communities reflected landscape characteristics and specific prey items
 available to wolves. Several parasite taxa identified in this study,
 including hookworms and coccidian protozoans, can cause morbidity and
 mortality in canids, especially in pups, or in combination with other
 stressors. The density-prevalence relationship for parasites with simple
 lifecycles may reflect a regulatory role of gastrointestinal parasites on
 wolf populations. Our result that faecal prevalence of parasites was lower
 in wolves with more diverse diets could provide insight into the
 mechanisms by which biodiversity may regulate disease. A diverse suite of
 predator-prey interactions could regulate the effects of parasitism on
 prey populations and mitigate the transmission of infectious agents,
 including zoonoses, spread via trophic interactions.
description: These data were collected as part of three previously published
 studies (see Related Works). The data come from the identification of
 gastrointestinal parasite larval stages (i.e., eggs, oocysts, sporocysts,
 and nematode larvae) using coprological methods in wolf feces. Samples
 came from the Abruzzo, Lazio and Molise National Park (PNALM) in Italy,
 Mercantour National Park (MNP) in France, the Northern Range of
 Yellowstone National Park (YNP) in the United States, the Great Bear
 Rainforest (GBR) on the west coast of Canada, and Riding Mountain National
 Park (RMNP) and Duck Mountain Provincial Park and Forest (DMPPF) in
 Canada.
DOI: 10.5061/dryad.m0cfxpp43
title: Cognition and covariance in the producer-scrounger game

description: 1. The producer-scrounger game is a key element of foraging ecology in
 many systems. Producing and scrounging typically covary negatively, but
 partitioning this covariance into contributions of individual plasticity
 and consistent between individual differences is key to understanding
 population level consequences of foraging strategies. Furthermore, little
 is known about the role cognition plays in the producer-scrounger game. 2.
 We investigated the role of cognition in these alternative foraging
 tactics in wild mixed-species flocks of great tits and blue tits, using a
 production learning task in which we measured individuals’ speed of
 learning to visit the single feeder in an array that would provide them
 with a food reward. We also quantified the proportion of individuals’
 feeds that were scrounges (‘proportion scrounged’); scrounging was
 possible if individuals visited immediately after a previous rewarded
 visitor. Three learning experiments–initial and two reversal
 learning–enabled us to estimate the repeatability and covariance of each
 foraging behaviour. 3. First, we examined whether individuals learned to
 improve their scrounging success (i.e. whether they actually obtained food
 by scrounging when there was an opportunity to do so). Second, we
 quantified the repeatability of proportion scrounged, and asked whether
 proportion scrounged affected production learning speed among individuals.
 Third, we used multivariate analyses to partition within- and
 among-individual components of covariance between proportion scrounged and
 production learning speed. 4. Individuals improved their scrounging
 success over time. Birds with a greater proportion scrounged took longer
 to learn their own rewarding feeder. Although multivariate analyses showed
 that covariance between proportion scrounged and learning speed was driven
 primarily by within-individual variation, that is, by behavioural
 plasticity, among-individual differences also played a role for blue tits.
 5. This is the first demonstration of a cognitive trait influencing
 producing and scrounging in the same wild system, highlighting the
 importance of cognition in the use of alternative resource acquisition
 tactics. The results of our covariance analyses suggest the potential for
 genetic differences in allocation to alternative foraging tactics, which
 are likely species and system dependent. They also point to the need to
 control for different foraging tactics when studying individual cognition
 in the wild.
DOI: 10.5061/dryad.kkwh70s4q
title: Deconstructing precipitation variability: Rainfall event size and timing uniquely alter ecosystem dynamics (Data)

description: This dataset contains data from a rainfall manipulation experiment
 described in the paper: "Griffin-Nolan, R.J., Slette, I.J. and Knapp,
 A.K. (2021), Deconstructing precipitation variability: rainfall event size
 and timing uniquely alter ecosystem dynamics. Journal of Ecology.
 https://doi.org/10.1111/1365-2745.13724" Water-limited ecosystems are
 highly sensitive to not only precipitation amount, but also precipitation
 pattern, particularly variability in the size and timing of growing season
 rainfall events. Both rainfall event size and timing are expected to be
 altered by climate change, but the relative responses of dryland
 ecosystems to changes in rainfall event size vs. timing has not been
 resolved. In this paper, we disentangle the effects of these different
 aspects of precipitation pattern on ecosystem dynamics. We experimentally
 assessed how these two aspects of rainfall variability impacted a
 semi-arid grassland ecosystem by altering an ambient precipitation pattern
 to eliminate variability in (1) rainfall event size (all events were made
 the same size), (2) rainfall event timing (all events were uniformly
 spaced in time), and (3) both. Total precipitation amount was constant for
 all treatments. We measured responses of soil moisture, ecosystem carbon
 flux (e.g., net primary production and soil CO2 flux), plant community
 composition, and physiological responses of the dominant C4 grass,
 Bouteloua gracilis. Removing variability in rainfall event size altered
 ecosystem dynamics more than a pattern of uniform event timing, but the
 largest impact occurred when variability in both were removed. Notably,
 eliminating variability in both event size and timing increased
 aboveground net primary productivity by 23%, consistent with reduced water
 stress in the dominant C4 grass, while also reducing seasonal variability
 in soil CO2 flux by 35%, reflecting lower seasonal variability in soil
 moisture. Synthesis: Unique responses to different aspects of
 precipitation variability highlight the complexity of predicting how
 dryland ecosystems will be affected by climate change induced shifts in
 rainfall patterns. Our results provide novel support for the key roles of
 rainfall event size and timing, in addition to total precipitation amount,
 as determinants of ecosystem function.
description: The dataset was collected during a field study at the Central
 Plains Experimentla Range (Colorado, USA) and has been processed by a
 series of linear mixed models (R, <i>lme4</i> package) to
 produce a manuscript accepted for publication in <em>Journal of
 Ecology</em>.
description: The readme file contains an explanation each datafile and
 associated units for each variable. Additional descriptions of the data
 are included in the shared R code,
 "final_analysis_051721.R". Information on how
 the measurements were done can be found in the associated manuscript
 referenced above.