cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bk3j9kj5
title: SSP: An R package to estimate sampling effort in studies of ecological communities

description: SSP (simulation-based sampling protocol) is an R package that uses
 simulations of ecological data and dissimilarity-based multivariate
 standard error (MultSE) as an estimator of precision to evaluate the
 adequacy of different sampling efforts for studies that will test
 hypothesis using permutational multivariate analysis of variance. The
 procedure consists in simulating several extensive data matrixes that
 mimic some of the relevant ecological features of the community of
 interest using a pilot data set. For each simulated data, several sampling
 efforts are repeatedly executed and MultSE calculated. The mean value,
 0.025 and 0.975 quantiles of MultSE for each sampling effort across all
 simulated data are then estimated and standardized regarding the lowest
 sampling effort. The optimal sampling effort is identified as that in
 which the increase in sampling effort does not improve the highest MultSE
 beyond a threshold value (e.g. 2.5 %). The performance of SSP was
 validated using real data. In all three cases, the simulated data mimicked
 the real data and allowed to evaluate the relationship MultSE – n beyond
 the sampling size of the pilot studies. SSP can be used to estimate sample
 size in a wide variety of situations, ranging from simple (e.g. single
 site) to more complex (e.g. several sites for different habitats)
 experimental designs. The latter constitutes an important advantage in the
 context of multi-scale studies in ecology. An online version of SSP is
 available for users without an R background.
description: The data for testing SSP were obtained from the following
 studies: 1. Ortigosa, D., Suárez-Mozo, N.Y., Barrera,
 N.C., and Simões, N. (2018). First survey of Interstitial molluscs from
 Cayo Nuevo, Campeche Bank, Gulf of Mexico. ZooKeys 779. doi:
 10.3897/zookeys.779.24562. 2. Ugalde, D., Gómez, P.,
 and Simoes, N. (2015). Marine sponges (Porifera: Demospongiae) from the
 Gulf of México, new records and redescription of Erylus trisphaerus (de
 Laubenfels, 1953). Zootaxa 3911(2), 151-183. doi:
 10.11646/zootaxa.3911.2.1. 3. Guerra-Castro, E.,
 Cruz-Motta, J.J., and Conde, J.E. (2011). Cuantificación de la diversidad
 de especies incrustantes asociadas a las raíces de Rhizophora mangle L. en
 el Parque Nacional Laguna de La Restinga. Interciencia 36(12),
 923-930.
description: To use the data mentioned above, please cite the respective
 bibliographic reference
DOI: 10.5061/dryad.jsxksn088
title: Empirical food webs of 12 tropical reservoirs in Singapore

description: We present 12 food webs from tropical reservoir communities in
 Singapore, and summarise the topology of each with widely used network
 indices (e.g., connectance, link density). Each reservoir was
 surveyed over 4–6 sampling occasions, during
 which, representative animal groups (i.e., fish species,
 and taxonomic/functional groups of zooplankton and benthic
 macroinvertebrates) and all likely sources of primary production (i.e.,
 macrophytes, periphyton, phytoplankton, and riparian terrestrial plants)
 were collected. We determined and measured gut content in fishes and bulk
 isotope (d13C and d15N) profiles of the animals collected, which
 contributed to estimating the relative strength of trophic relationships
 using Bayesian mixing models. We document our protocol here, alongside a
 script in the R programming language for executing data
 management/analyses/visualisation procedures used in our
 study. This data can be used to glean insights into
 trends in inter- and intra-specific or guild interactions in analogous
 freshwater lake habitats.
description: Please see the associated published article for details.
DOI: 10.5061/dryad.tdz08kpzm
title: Microsatellites for northern pike (Esox lucius) populations in Germany

description: Esox lucius L. (northern pike) inhabits river, lake and brackish water
 ecosystems of the temperate region in North America and Eurasia. In many
 areas of its native range, the species is confronted with human-induced
 disturbances that can affect local and regional genetic diversity.
 Conservation of genetic diversity constitutes an important policy
 objective. Therefore, we investigated how the genetic population structure
 and patterns suggestive of hybridization among subpopulations from
 different catchments vary with the type of ecosystem (river vs. lake) and
 the integrity of the ecosystem assessed using ecological status
 assessments of the European Water Framework Directive (WFD) and indices of
 the wetland quality (in rivers) and trophic state (in lakes). 1,384 pike
 samples from the North, Baltic and Black Sea drainages in Germany were
 analysed. We differentiated between metapopulations from each
 hydrogeographic region using genotypes from 15 microsatellites and
 mitochondrial cyt b sequences. Individual populations showed signs of
 genetic admixture ranging from almost zero to complete replacement by
 foreign genotypes originating from different catchments. Hierarchical
 general linear modeling revealed a significantly positive association of
 the degree of genetic hybridization with decreasing ecological status. An
 eroded population substructure indicative of hybridization was also
 significantly elevated in rivers relative to lakes and in heavily modified
 water bodies. Results were consistent when using ecological status
 assessments by the WFD and an alternative environmental quality index
 based on the health of wetlands in rivers and trophic state in lakes. We
 speculate that macrophyte loss through loss of wetlands or in response to
 eutrophication fostered genetic mixing among different subpopulations,
 which were brought into secondary contact either due to stocking or due to
 natural dispersal from foreign catchments. Our findings suggest that
 anthropogenic alteration of freshwater ecosystems may influence the
 genetic structures present in a freshwater top piscivore at both local and
 regional scales.
description: Samples of individual pike collected across a multitude of lakes
 and rivers in Germany and genotyped using 15 microsatellites.
DOI: 10.5061/dryad.280gb5mp8
title: Moving academic conferences online: understanding patterns of delegate engagement

description: Scientific conferences are a key component of academic communication and
 development. During the COVID-19 pandemic in-person conferences are
 rapidly moving online, yet these virtual events may not provide the same
 opportunities as in-person conferences. If virtual meetings are to
 continue to provide effective communication and networking between
 researchers and stakeholders, they must be adapted to increase delegate
 engagement and enthusiasm. Here we present a case study of a recent
 medium-sized online conference. We assessed the behaviour and engagement
 of delegates with different components of the meeting using data from
 website analytics and post-conference surveys. Behaviour was variable
 across the available events, with talks being particularly popular but
 engagement with social and networking opportunities was variable. Our
 conclusions have been summarised in six recommendations to support future
 online conference organisers in enhancing engagement with their events.
description: These datasets were collected after an online conference using
 two different methods: website analytics (from delegates that had accepted
 website cookies); twitter analytics; and a post-conference questionnaire.
 Analytic data were not processed in any way other than cleaning and
 formatting. Questionnaire data have the free text data removed in order to
 keep the data confidential.
description: ReadMe file has been uploaded in order to guide users.
DOI: 10.6078/d1wb0s
title: Inferring core processes using stochastic models of the geodynamo

description: Recent studies have represented time variations in the Earth's axial
 magnetic dipole field as a stochastic process, which comprises both
 deterministic and random elements. To explore how these elements are
 affected by the style and vigor of convection in the core, as well as the
 core-mantle boundary conditions, we construct stochastic models from a set
 of numerical dynamo simulations at low Ekman numbers. The deterministic
 part of the stochastic model, the drift term, characterises the slow
 relaxation of the dipole back to its time average. We find that these
 variations are predominantly accommodated by the slowest decay
 mode, enhanced by turbulent diffusion to enable a faster
 relaxation. The random part—the noise term—is set by the amplitude and
 timescale of variations in dipole field generation, including
 contributions from both velocity and internal magnetic field
 variations.  Applying these interpretations to the paleomagnetic
 field suggests that reversal rates are very sensitive to rms variations in
 the source. Less than a 50 percent reduction in rms source variations is
 sufficient to prevent reversals for the recent magnetic field.
description: This dataset was generated using the numerical geodynamo
 simulation software CALYPSO
 (https://geodynamics.org/cig/software/calypso/).
DOI: 10.5061/dryad.v9s4mw6tt
title: Prenatal auditory learning in avian vocal learners and non-learners

description: Understanding when learning begins is critical for identifying the factors
 that shape both the developmental course and the function of information
 acquisition. Until recently, sufficient development of the neural
 substrates for any sort of vocal learning to begin in songbirds was
 thought to be reached well after hatching. New research shows that
 embryonic gene activation and the outcome of vocal learning can be
 modulated by sound exposure in ovo. We tested whether avian embryos across
 lineages differ in their auditory response strength and sound learning in
 ovo, which we studied in vocal learning (Maluridae, Geospizidae) and vocal
 non-learning (Phasianidae, Spheniscidae) taxa. While measuring heart rate
 in ovo, we exposed embryos to (1) conspecific or heterospecific
 vocalisations, to determine their response strength, and (2) conspecific
 vocalisations repeatedly, to quantify cardiac habituation, a form of
 non-associative learning. Response strength towards conspecific
 vocalisations was greater in two species with vocal production learning
 compared to two species without. Response patterns consistent with
 non-associative auditory learning occurred in all species. Our results
 demonstrate a capacity to perceive and learn to recognise sounds in ovo,
 as evidenced by habituation, even in species that were previously assumed
 to have little, if any, vocal production learning.
DOI: 10.5061/dryad.b2rbnzsdc
title: Data to replicate: Forecasting community reassembly using climate-linked spatio-temporal ecosystem models

description: Ecosystems are increasingly impacted by human activities, altering
 linkages among physical and biological components. Spatial community
 reassembly occurs when these human impacts modify the spatial overlap
 between system components, and there is need for practical tools to
 forecast spatial community reassembly at landscape scales using monitoring
 data. To illustrate a new approach, we extend a generalization of
 empirical orthogonal function (EOF) analysis, which involves a
 spatio-temporal ecosystem model that approximates coupled physical,
 biological, and human dynamics. We then demonstrate its application to
 five trophic levels for the eastern Bering Sea by fitting to multiple,
 spatially unbalanced datasets measuring physical characteristics
 (temperature measurements and climate-linked forecasts), primary producers
 (spring and fall size-fractionated chlorophyll-a), secondary producers
 (copepods), juveniles (age-0 walleye pollock), adult consumers (five
 commercially important fishes), human activities (seasonal fishing
 effort), and mobile predators (seabirds). We identify the spatial niche
 for each ecosystem component, as well as dominant modes of variability
 that are highly correlated with a known bottom-up driver of dynamics. We
 then measure spatial overlap between interacting variables (using
 Schoener’s-D) and identify that age-0 pollock have decreased spatial
 overlap with copepods and increased overlap with adult pollock during warm
 years, and also that adult pollock have increased overlap with arrowtooth
 flounder and decreased overlap with catcher-processor fishing effort
 during these warm years. Given the warming conditions that are projected
 for the coming decade, the model forecasts increased prey and competitor
 overlap involving adult pollock (between age-0 pollock, adult pollock and
 arrowtooth flounder) and decreased overlap with the copepod forage base
 and with the catcher-processor fishery during future warming. We recommend
 that joint species distribution models be extended to incorporate
 “ecological teleconnections” (correlations between distant locations
 arising from known mechanisms) arising from behavioral adaptation by
 mobile animals as well as passive advection of nutrients and planktonic
 juvenile stages.
description: All data were collected by previous governmental programs, and
 were described in the main text and appendices.
description: The data set does not include the Catcher-Processor data used in
 the manuscript.  Those data are proprietary commercial information.  For
 those data, please contact Alan Haynie (alan.haynie@noaa.gov)
DOI: 10.5061/dryad.pvmcvdnk6
title: Did shell-crushing predators drive the evolution of ammonoid septal shape?

description: For centuries, paleontologists have sought functional explanations for the
 uniquely complex internal walls (septa) of ammonoids, extinct shelled
 cephalopods. Ammonoid septa developed increasingly complex fractal
 margins, unlike any modern shell morphologies, throughout more than 300
 million years of evolution. Some have suggested these morphologies
 provided increased resistance to shell-crushing predators. We perform the
 first physical compression experiments on model ammonoid septa using
 controlled, theoretical morphologies generated by computer-aided design
 and 3D printing. These biomechanical experiments reveal that increasing
 complexity of septal margins does not increase compression resistance. Our
 results raise the question of whether the evolution of septal shape may be
 tied closely to the placement of the siphuncle foramen (anatomic septal
 hole). Our tests demonstrate weakness in the centers of uniformly thick
 septa, supporting work suggesting reinforcement by shell-thickening at the
 center of septa. These experiments highlight the importance of 3D
 reconstruction using idealized theoretical morphologies that permit the
 testing of long-held hypotheses of functional evolutionary drivers by
 recreating extinct morphologies once rendered physically untestable by the
 fossil record.
description: <b>Figure S1.</b> <b>Materials test of rigid
 resin.</b> Load versus displacement curved for models cured at 80°C
 for (A) 15 minutes, (B) 30 minutes, (C) 45 minutes, (D) 60 minutes, (E)
 120 minutes, (F) 180 minutes. <b>Figure S2.
 Generalized depiction of the box method of fractal analysis modified from
 Peterman and Barton 2019.</b> For methodological details and
 original figure see Peterman and Barton 2019.
 <b>Figure S3. Septal shape and shell strength with genera
 grouped by shape. </b>Peak load sustained by each genus with (A)
 ammonitic septa, (B) ceratitic septa, (C) goniatitic septa, (D) nautiloid
 septa. Red triangles represent average peak load for each genus. Red
 dotted line represents average peak load for septal shape type.
DOI: 10.5061/dryad.nvx0k6drf
title: Evolution of songbird eggs colour

description: To understand why avian eggs are so variable in colour and patterning, we
 investigated contemporary species that provide insights into the
 evolutionary transitions that occurred during the early radiation of the
 songbirds. We quantified egg colour and patterning from museum collections
 of 269 species of Australian passerine and collated it to nest type data
 (cup or dome nesting species). Using phylogenetically reconstructed trait
 data, we showed that the ancestral passerine egg was likely to be white,
 and to have been laid inside a domed nest. Egg colouration and nest type
 were both phylogenetically clustered, and there was evidence of correlated
 evolution between the two traits. As nests transitioned from domes to
 cups, there was an increase in the range of egg colours observed,
 presumably as a response to additional stressors. Finally, we found that
 egg colour changes occurred more than twice as frequently in cup nesting
 species than in dome nesting species. This suggests that cup-nesting
 species may be using colour as an adaptive trait to compensate for the
 loss of the protective nest roof.
DOI: 10.5061/dryad.ffbg79ctc
title: Genome, annotations and SNPs for the green peafowl and associated scripts

description: Both anthropogenic impacts and historical climate change could contribute
 to population decline and species extinction, but their relative
 importance has yet to be determined. Emerging approaches based on genomic,
 climatic and anthropogenic data provide a promising analytical framework
 to address this question. This study applied such an integrative approach
 to examine potential drivers for endangerment of the green peafowl (Pavo
 muticus). Several demographic reconstructions based on population genomes
 congruently retrieved a drastic population declination since the
 mid-Holocene. Furthermore, comparison between historical and modern
 genomes suggested genetic diversity decrease during the last 50 years.
 However, climate-based ecological niche models predicted general range
 stationarity during these periods and imply little impact of climate
 change. Further analyses suggested that human activity intensities were
 negatively correlated with the green peafowl’s effective population sizes
 and significantly associated with its survival statuses (extirpation or
 persistence). Archaeological and historical records corroborate the
 critical role of humans, leaving the footprint of low genomic diversity
 and high inbreeding in the surviving populations. This study sheds light
 on the potential deep-time effects of human disturbance on species
 endangerment and on the whole, offers immediately a multi-evidential
 approach in examining underlying forces for population declines.
description: The pseudo-chromosomes
 were generated
 by mapping assembled scaffolds of the green peafowl's genome assembly
 (GenBank accession: JACDJE000000000) into of the chicken assembly (GenBank
 accession: GCA_000002315.5,
 hereafter the chicken genome) via synteny using Chromosemble in Satsuma
 v2.0. The annotations were obtained using MAKER v2.31.10.
DOI: 10.5061/dryad.5x69p8d24
title: Moisture and mold-proof characteristics of surface modified wood for musical instrument soundboards

description: Wood is the major material for musical instrument soundboards fabrication
 on account of practical and cultural reasons. However, as a natural
 material, wood is easy to be degraded due to moisture or fungi corrosion.
 The traditional wood protection methods are normally meant for the
 structural materials, which might not suitable for the soundboard
 materials. Therefore, in this work, a novel nanomaterial-based
 modification method was applied to effectively protect wood from moisture
 and fungi, without causing changes to the acoustic properties of wood. The
 modified wood could do a better work in constructing soundboards with long
 lifespan.
DOI: 10.25338/b8k917
title: Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly

description: This dataset contains a single whole-genome optical map file (.CMAP) for
 bread wheat (Triticum aestivum) cv Chinese Spring (CS). The methods for
 constructing this optical map and the properties of this map are described
 below. The definition of the CMAP format is documented
 in https://bionanogenomics.com/wp-content/uploads/2017/03/30039-CMAP-File-Format-Specification-Sheet.pdf.  The extracted ultra-high-molecular weight DNA molecules of CS were labeled with the DLE-1 enzyme (Bionano Genomics, San Diego, CA, USA) and were then stained with the Bionano PrepTM DLS Kit (Bionano Genomics, San Diego, CA, USA). A consensus optical map was de novo assembled with the Assembler tool of the Bionano Solve v3.3 package using significance cutoffs of P &lt; 1 × 10-11 to generate draft consensus contigs, P &lt; 1 × 10-12 for draft consensus contig extension, and P &lt; 1 × 10-16 for final merging of the draft consensus contigs. A recipe of “nonhaplotype”, “noES”, and “noCut” was chosen. The initial optical map was then checked for potential chimeric contigs. Images of DLE-1-labeled CS DNA molecules &gt; 150 kb and equivalent to about 136x genome coverage were collected and assembled into a whole-genome optical map. The map contained 726 contigs with an N50 of 55.01 Mb and a total length of 14.41 Gb.
DOI: 10.5061/dryad.18931zcwb
title: Urban forests host rich polypore assemblages in a Nordic metropolitan area

description: This dataset contains data for a manuscript titled 'Urban
 forests host rich polypore assemblages in a Nordic metropolitan area'
 where we have studied associations between the diversity
 of dead-wood inhabiting fungi and urbanization.
 The included spreadsheets contain data used in the analyses, i.e.
 polypore species occurrences, species richness and
 environmental data, accompanied by annotations about the characteristics
 of the study sites and individual dead-wood units. Data is given at two
 spatial scales on two separate spreadsheets: one at the level of dead-wood
 units and the other at the level of forest stands.
 Variable explanations are provided in separate text files. For further
 details regarding data collection and processing, please see the published
 article (https://doi.org/10.1016/j.landurbplan.2021.104222).
description: Variable explanations are provided in separate text files (titled
 'Variable_xplanations_for_table_ ... .txt'). Please, see the
 published article (https://doi.org/10.1016/j.landurbplan.2021.104222) for
 further details regarding data collection and processing.
DOI: 10.5061/dryad.wpzgmsbm2
title: Full data on telomere length and lifespan

description: Telomeres are protective caps at the end of eukaryotic chromosomes that
 shorten with age and in response to stressful or resource-demanding
 conditions. Their length predicts individual health and lifespan across a
 wide range of animals, but whether the observed positive association
 between telomere length and lifespan is environmentally induced, or set at
 conception due to a shared genetic basis, has not been tested in wild
 animals. We applied quantitative genetic ‘animal models’ to longitudinal
 telomere measurements collected over a 10-year period from individuals of
 a wild seabird (common tern; Sterna hirundo) with known pedigree. We found
 no variation in telomere shortening with age among individuals at the
 phenotypic and genetic level, and only a small permanent environmental
 effect on adult telomere length. Instead, we found telomere length to be
 highly heritable and strongly positively genetically correlated with
 lifespan. Such heritable differences between individuals that are set at
 conception may present a hitherto underappreciated component of variation
 in somatic state.