cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cjsxksn6t
title: Data for: Should I breed or should I go? Manipulating individual state during migration influences breeding decisions in a long-lived bird species

description: Documentation of Carry-Over Effects (COEs), defined as effects resulting
 from events that occurred in a previous time period, has largely been
 observational and understanding of specific mechanisms underlying COEs is
 still lacking. To investigate this, we simulated an environmental
 perturbation during the spring migration of a long-lived bird species and
 looked at the subsequent effects on various breeding parameters. We
 captured female greater snow geese (Anser caerulescens atlanticus) on
 their spring staging sites and maintained individuals in captivity for up
 to four days before releasing them. We re-observed females 3000 km North,
 on their Arctic breeding grounds, to estimate their breeding propensity
 (i.e., probability of initiating a reproductive event for a given year),
 and measure their arrival date, laying date, clutch size, and nesting
 success. Only proxies of breeding propensity were affected by our
 manipulation, which decreased as the time spent in captivity increased.
 However, females were able to overcome the effects of captivity in two out
 of the three years of experimentation with normal or good environmental
 conditions at the breeding site. When facing the additional challenge of
 poor environmental conditions, many individuals manipulated during
 migration apparently curtailed their reproductive effort by skipping
 breeding. This experiment is the first to show that breeding propensity is
 an important parameter affected by COEs resulting from stressful events
 prior to reproduction in long-lived species.
DOI: 10.5068/d1v68x
title: International COVID-19 mortality forecast visualization: covidcompare.io

description: COVID-19 mortality forecasting models provide critical information about
 the trajectory of the pandemic, which is used by policymakers and public
 health officials to guide decision-making. However, thousands of published
 COVID-19 mortality forecasts now exist, many with their own unique
 methods, assumptions, format, and visualization. As a result, it is
 difficult to compare models and understand under which circumstances a
 model performs best. Here, we describe the construction and usability of
 covidcompare.io, a web tool built to compare numerous forecasts and offer
 insight into how each has performed over the course of the pandemic. From
 its launch in December 2020 to June 2021, we have seen 4,600 unique
 visitors from 85 countries. A study conducted with public health
 professionals showed high usability overall as formally assessed using a
 Post-Study System Usability Questionnaire (PSSUQ). We find that
 covidcompare.io is an impactful tool for the comparison of international
 COVID-19 mortality forecasting models.
description: During a recorded Zoom call, participants were asked to perform a
 series of tasks on covidcompare.io after which they were administered the
 PSSUQ via Qualtrics to assess website usability. The Zoom calls were no
 longer than one hour each.
description: The PSSUQ is a 19-item validated questionnaire with likest-scale
 responses (1 to 7); answers of value 8 indicate that the question is
 "Not Applicable". For more information refer to:
 Lewis JR. Psychometric Evaluation of the Post-Study System
 Usability Questionnaire: The PSSUQ. Proc Hum Factors Ergonomics Soc Annu
 Meet 1992;36:1259--1260. doi:10.1177/154193129203601617
DOI: 10.5061/dryad.573n5tb8x
title: Scores from S.invicta queen supergene pheromone discrimination assays

description: Ants use chemical signals to communicate for various purposes related to
 colony function. Social organization in the red imported fire
 ant, Solenopsis invicta, is determined by
 the Sb supergene, with colonies of the monogyne
 (single-queen) form lacking the element and colonies of the polygyne
 (multiple-queen) form possessing it. Polygyne workers accept new
 reproductive queens in their nest, but only those carrying Sb;
 young winged queens lacking this genetic element are executed as they
 mature sexually in their natal nest or as they attempt to enter a foreign
 nest to initiate reproduction after mating and shedding their wings. It
 has been suggested that queen supergene genotype status is signaled to
 workers by unsaturated cuticular hydrocarbons, while queen reproductive
 status is signaled by piperidines (venom alkaloids). We used
 high-throughput behavioral assays to study worker acceptance of paper
 dummies dosed with fractions of extracts of polygyne queens, or blends of
 synthetic counterparts of queen cuticular compounds. We show that the
 queen supergene pheromone comprises a blend of monoene and diene
 unsaturated hydrocarbons. Our assays also reveal that unsaturated
 hydrocarbons elicit discrimination by polygyne workers only when
 associated with additional compounds that signal queen fertility. This
 synergistic effect was obtained with a polar fraction of queen extracts,
 but not by the piperidine alkaloids, suggesting that the chemical(s)
 indicating queen reproductive status are compounds more polar than
 cuticular hydrocarbons but are not the piperidine alkaloids. Our results
 advance understanding of the role of chemical signaling that is central to
 the regulation of social organization in an important invasive pest and
 model ant species.
description: The dataset comprises the details of each behavioral assay
 conducted, including time (year), colony ID, and retrieval time of each
 dummy (or corpse). The scoring metric is explained in the method section
 of the paper.
description: Please refer to the ReadMe file.
DOI: 10.5061/dryad.g1jwstqs8
title: Sleep hygiene knowledge and engagement in Australian shift workers

description: Objectives: Shiftworkers routinely obtain inadequate sleep, which has
 major health consequences. Sleep hygiene describes a range of behaviours,
 lifestyle and environmental factors that can improve sleep. To date,
 limited research has examined sleep hygiene in shiftworkers. This study
 aimed to assess the sociodemographic and behavioural correlates of sleep
 hygiene knowledge and engagement with sleep hygiene practices in
 Australian shiftworkers. Study Design: An online, cross-sectional survey.
 Setting and Participants: Australian adults from across multiple
 industries (n = 588) who work shift work. Measures: The online survey
 included questions regarding sleep hygiene knowledge, and questions from
 modified versions of the Pittsburgh Sleep Quality Index and Sleep Hygiene
 Index. Results: Of the 588 participants, 52.9% reported having heard of
 ‘sleep hygiene’. Of these participants, 77.5% reported understanding the
 term moderately, extremely or very well. Engagement with each sleep
 hygiene practice was varied. Common sleep hygiene practices were
 controlling the bedroom environment (e.g., a cool, dark and quiet
 bedroom). Less common practices were avoiding light as bedtime approaches.
 Logistic regressions revealed that shiftworkers who had heard of sleep
 hygiene were more likely to engage in sleep hygiene practices and had
 better sleep quality compared to those who had not heard of sleep hygiene.
 Increased engagement in sleep hygiene practices did not predict the
 likelihood of individuals reporting better sleep quality. Conclusions:
 Shiftworkers demonstrated varied knowledge, understanding and engagement
 with individual sleep hygiene practices. Future research should focus on
 the development of sleep hygiene interventions that accommodate the unique
 challenges of shift work to optimise sleep.
description: The data was collected through an anonymous online survey
 using Qualtrics (Version [XM] Copyright © 2020) and divided into three
 sections; i) demographic and work characteristics, ii) sleep hygiene
 knowledge and practices, and iii) sleep quantity and quality. The survey
 included a total of 29 questions drawn from the Pittsburgh Sleep Quality
 Index (PSQI) , as well as, questions modified from the Sleep Hygiene Index
 (SHI). The data was exported into and excell
 spreadsheet for cleaning, the uploaded to SPSS for analysis.
DOI: 10.5061/dryad.fn2z34tvx
title: Gene flow influences the genomic architecture of local adaptation in six riverine fish species

description: Understanding how gene flow influences adaptive divergence is important
 for predicting adaptive responses. Theoretical studies suggest that when
 gene flow is high, clustering of adaptive genes in fewer genomic regions
 would protect adaptive alleles from recombination and thus be selected
 for, but few studies have tested it with empirical data. Here, we used
 RADseq to generate genomic data for six fish species with contrasting life
 histories from six reaches of the Upper Mississippi River System, USA. We
 used four differentiation-based outlier tests and three
 genotype-environment association analyses to define neutral SNPs and
 outlier SNPs that were putatively under selection. We then examined the
 distribution of outlier SNPs along the genome and investigated whether
 these SNPs were found in genomic islands of differentiation and
 inversions. We found that gene flow varied among species, and outlier SNPs
 were clustered more tightly in species with higher gene flow. The two
 species with the highest overall FST (0.0303 - 0.0720) and therefore
 lowest gene flow showed little evidence of clusters of outlier SNPs, with
 outlier SNPs in these species spreading uniformly across the genome. In
 contrast, nearly all outlier SNPs in the species with the lowest FST
 (0.0003) were found in a single large putative inversion. Two other
 species with intermediate gene flow (FST ~ 0.0025 - 0.0050) also showed
 clustered genomic architectures, with most islands of differentiation
 clustered on a few chromosomes. Our results provide important empirical
 evidence to support the hypothesis that increasingly clustered
 architectures of local adaptation are associated with high gene
 flow.
DOI: 10.5061/dryad.vmcvdncv1
title: Data for: Evaluating the impact of anatomical partitioning on summary topologies obtained with Bayesian phylogenetic analyses of morphological data

description: Morphological data are a fundamental source of evidence to reconstruct the
 Tree of Life, and Bayesian phylogenetic methods are increasingly being
 used for this task. Bayesian phylogenetic analyses require the use of
 evolutionary models, which have been intensively studied in the past few
 years, with significant improvements to our knowledge. Notwithstanding, a
 systematic evaluation of the performance of partitioned models for
 morphological data has never been performed. Here we evaluate the
 influence of partitioned models, defined by anatomical criteria, on the
 precision and accuracy of summary tree topologies considering the effects
 of model misspecification. We simulated datasets using partitioning
 schemes, trees, and other properties obtained from two empirical datasets,
 and conducted Bayesian phylogenetic analyses. Additionally, we reanalysed
 32 empirical datasets for different groups of vertebrates, applying
 unpartitioned and partitioned models, and, as a focused study case, we
 reanalysed a dataset including living and fossil armadillos, testing
 alternative partitioning hypotheses based on functional and ontogenetic
 modules. We found that, in general, partitioning by anatomy has little
 influence on summary topologies analysed under alternative partitioning
 schemes with a varying number of partitions. Nevertheless, models with
 unlinked branch lengths, which account for heterotachy across partitions,
 improve topological precision at the cost of reducing accuracy. In some
 instances, more complex partitioning schemes, led to topological changes,
 as tested for armadillos, mostly associated with models with unlinked
 branch lengths. We compare our results with other empirical evaluations of
 morphological data and those from empirical and simulation studies of
 partitioning of molecular data, considering the adequacy of anatomical
 partitioning relative to alternative methods of partitioning morphological
 datasets.
DOI: 10.5061/dryad.f1vhhmgzb
title: Data from: The active mouse rests within: Energy management among and within individuals

description: 1. The relationship between daily energy expenditure (DEE) and resting
 metabolic rate (RMR) provides insight into how organisms allocate energy
 to maintenance versus energetically expensive activities such as locomotor
 activity. 2. Three models have been devised to describe energy management:
 the allocation, independent, and performance models, which respectively
 predict a DEE-RMR slope of b&lt;1, b=1, and b&gt;1. 3. Here, we
 took paired repeated metabolic and behavioural measurements in 51 female
 white-footed mice to 1) evaluate which energy management models apply at
 the among- and within-individual levels, and to 2) quantify the
 relationship between metabolic traits and two energetically expensive
 behaviours. 4. The DEE-RMR slope was different at the among- versus
 within-individual levels, with values supporting the performance and
 allocation models at the among- and within-individual levels,
 respectively. Accordingly, the relationship between voluntary wheel
 running and RMR was positive at the among-individual level (r =
 0.40±0.21), but negative at the within-individual level (r ­= -0.23±0.10).
 5. To our knowledge, this is the first study to simultaneously partition
 the relationship between RMR and behaviour at the among- versus
 within-individuals levels while determining which energy management models
 apply at each of these levels. In doing so, we have identified a mechanism
 through which compensation occurs at the within-individual level.
description: See paper.
description: See ReadMe.txt file.
DOI: 10.6086/d13h4p
title: Bumble bee (B. vosnesenskii) queen nest searching occurs independent of ovary developmental status

description: Studies on the physiological states of wild-caught organisms are essential
 to uncovering the links between ecological and physiological
 processes. Bumble bee queens emerge from overwintering in the
 spring. At this time, queens develop their ovaries and search for a nest
 site in which to start a colony. Whether these two processes, ovary
 development and nest-searching, interact with or influence one another
 remains an unresolved question in behavioral physiology. We explored the
 hypothesis that ovary development and nest-searching might be
 mechanistically connected, by testing whether (1) ovary development
 precedes nest-searching behavior; (2) nest occupation precedes ovary
 development; or (3) ovary development and nest-searching occur
 independently, in bumble bee (Bombus vosnesenskii) queens.  We
 collected queens either nest-searching (and thus prior to occupying a
 nest) or pollen-collecting (and thus provisioning an occupied nest) and
 measured their degree of ovary activation. We further screened these
 queens for parasites or other symbionts, to identify additional factors
 that may impact their reproductive success at this time. We found that
 queens searched for and occupied nests at all stages of ovary development,
 indicating that these processes occur independently in this system.
 Nest-searching queens were more likely to have substantial mite loads than
 pollen-collecting queens, who had already located and occupied a nest.
 However, mite loads did not significantly predict ovary developmental
 status. Collectively, our work shows that nesting status and symbionts
 alone are insufficient to explain the variation in spring bumble bee queen
 ovary development. We propose that ovary development and nest-searching
 occur opportunistically, which may enable queens to begin laying eggs
 earlier in the season than if these processes occurred in discrete
 succession.
description: data collection described in manuscript
DOI: 10.5061/dryad.w3r2280s2
title: Comet fading begins beyond Saturn

description: The discovery probability of long-period comets (LPCs) passing near the
 Sun is highest during their first passage and then declines, or fades,
 during subsequent return passages. Comet fading is largely attributed to
 devolatilization and fragmentation via thermal processing within 2-3 AU of
 the Sun (1 AU being the Earth-Sun distance). Here our numerical
 simulations show that comet observing campaigns miss vast numbers of LPCs
 making returning passages through the Saturn region (near 10 AU) because
 these comets fade during prior, even more distant passages exterior to
 Saturn and thus elude detection. Consequently, comet properties
 significantly evolve at solar distances much larger than previously
 considered, and this offers new insights into the physical and dynamical
 properties of LPCs, both near and far from Earth.
description: This is dynamical computer simulation data generated via 2-Gyr
 runs of long-period comet production using the SCATR code.
description: Included are the raw simulation results of comet production along
 with the python script ('fancyplotbuilder.py') needed to
 generate each figure in the main paper. Simulation set is divided into 100
 subsimulation directories that are co-added to comprise a single
 simulation.
DOI: 10.5061/dryad.xsj3tx9gq
title: Bone structural data for the Denver Longitudinal Growth Study

description: Long bone structural dimensions have been shown to be responsive to
 mechanical loadings during life. Thus, they can be used to track
 behavioral changes as well as changes in body size during ontogeny.
 Radiographic measurements of long bone structural properties (lengths,
 cross-sectional geometric properties, articular breadths) were carried out
 for a sample of 20 children who had participated in the Denver Growth
 Study. An average of 36 longitudinal time points for each individual,
 taken at 6-month intervals between early infancy and late adolescence,
 were included. Anthropometric and muscle area dimensions were also
 available. The data have been previously used in a range of studies,
 including growth changes in bone strength, adaptation to bipedalism, and
 body size prediction in juveniles.
description: Data were collected from radiographs taken as part of the Denver
 Growth Study, which was carried out in the 1930s-1960s. Long bone lengths,
 articular breadths, and diaphyseal total and cortical breadths of the
 femur and humerus were measured, with the latter used to derive section
 properties (measures of bone rigidity and strength). Please see the ReadMe
 file for more methodological details.
description: Two files are provided, one with and one without interpolations
 for missing data. Please see the ReadMe file for more
 information.
DOI: 10.6078/d1hb0c
title: A large-scale microelectromechanical-systems-based silicon photonics LiDAR

description: Three-dimensional (3D) imaging sensors enable machines to perceive, map,
 and interact with the surrounding world. The size of light detection and
 ranging (LiDAR) devices is often limited by mechanical scanners. Focal
 plane array-based 3D sensors are promising candidates for solid-state
 LiDARs because they enable electronic scanning without mechanical moving
 parts, however, their resolutions have been limited to 512 pixels or
 smaller. In this paper, we report on a 16,384-pixel LiDAR with a wide
 field of view (70°×70°), a fine addressing resolution (0.6°×0.6°), a
 narrow beam divergence (0.050°×0.049°), and a random-access beam
 addressing with sub-MHz operation speed. The 128×128-element focal plane
 switch array (FPSA) of grating antennas and micro-electro-mechanical
 system (MEMS)-actuated optical switches are monolithically integrated on a
 10×11 mm2 silicon photonic chip, where a 128×96 sub-array is wire-bonded
 and tested in experiments. 3D imaging with a distance resolution of 1.7 cm
 is achieved with frequency-modulated continuous-wave (FMCW) ranging in
 monostatic configuration. The FPSA can be mass-produced in complementary
 metal-oxide-semiconductor (CMOS) foundries, which will enable ubiquitous
 3D sensors for autonomous cars, drones, robots, and smartphones.
DOI: 10.5061/dryad.rjdfn2zcg
title: Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa

description: Many highly social species show plasticity in their social structure in
 response to different environmental conditions. For example,
 typical colonies of the yellowjacket wasp Vespula squamosa are headed by a
 single reproductive queen and survive for only a single season. However,
 in warmer climates, V. squamosa colonies sometimes persist for multiple
 years and can grow to extremely large size. We used genetic markers to
 understand patterns of reproduction and recruitment within these perennial
 colonies. We genotyped V. squamosa workers, pre-reproductive queens, and
 males from perennial colonies in the southeastern United States at 10
 polymorphic microsatellite loci and one mitochondrial DNA locus. We found
 that V. squamosa from perennial nests were produced by multiple
 reproductives, in contrast to typical annual colonies. Relatedness of
 nestmates from perennial colonies was significantly lower than relatedness
 of nestmates from annual colonies. Our analyses of mitochondrial DNA
 indicated that most V. squamosa perennial colonies represented semi-closed
 systems whereby all individuals belonged to a single matriline despite the
 presence of multiple reproductive females. However, new queens
 recruited into perennial colonies apparently mated with non-nestmate
 males. Notably, perennial and annual colonies did not show
 significant genetic differences, supporting the hypothesis that perennial
 colony formation represents an instance of social phenotypic
 plasticity. Overall, our results indicate that perennial V.
 squamosa colonies show substantial changes to their social biology
 compared to typical annual colonies.
description: PCRs were used to amplify DNA at 10 microsatellite loci. PCRs
 were generally conducted in a final volume of 15 μL composed of: 6.4 μL
 deionized water, 2.4 μL 25mM MgCl2, 1.5 μL 10x PCR buffer, 1.2 μL 2.5mM
 dNTPs, 1 μL Taq polymerase, 0.75 μL each of 10 μM reverse and
 fluorescence-tagged forward primers, and 1 μL of DNA. The PCR
 amplification profile used for each locus was: 2 min at 94°C, 35 cycles
 for 30 sec at 94°C, 30 sec at locus-specific annealing temperature (Table
 2), 30 sec at 72°C, and then a final extension for 5.5 min at 72°C. PCR
 products were run on a 3% agarose gel at 100V to verify amplification for
 each individual. After confirmation of amplification,
 microsatellite genotypes were analyzed using the fragment analysis module
 of an ABI 3100 sequencer. Scoring was completed using a combination of
 GeneMapper v4.0 (Applied
 Biosystems, Foster City, CA) and manual scoring of
 peaks.
description: Data are in Genepop format (i.e. 185/189 -&gt; 185189).
 Haploid males are represented as diploid with their allele doubled (i.e.
 185 -&gt; 185185).