cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.280gb5mqs
title: Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life

description: Until recently, most viruses detected and characterized were of economic
 significance, associated with agricultural and medical diseases. This was
 certainly true for the eukaryote-infecting circular Rep
 (replication-associated protein)-encoding single-stranded DNA (CRESS DNA)
 viruses, which were thought to be a relatively small group of viruses.
 With the explosion of metagenomic sequencing over the past decade and
 increasing use of rolling-circle replication for sequence amplification,
 scientists have identified and annotated copious numbers of novel CRESS
 DNA viruses – many without known hosts but which have been found in
 association with eukaryotes. Similar advances in cellular genomics have
 revealed that many eukaryotes have endogenous sequences homologous to
 viral Reps, which not only provide “fossil records” to reconstruct the
 evolutionary history of CRESS DNA viruses but also reveal potential host
 species for viruses known by their sequences alone. The Rep protein is a
 conserved protein that all CRESS DNA viruses use to assist rolling circle
 replication that is known to be endogenized in a few eukaryotic species
 (notably tobacco and water yam). A systematic search for endogenous
 Rep-like sequences in GenBank’s non-redundant eukaryotic database was
 performed using tBLASTn. We utilized relaxed search criteria for the
 capture of integrated Rep sequence within eukaryotic genomes, identifying
 93 unique species with an endogenized fragment of Rep in their nuclear (78
 species), plasmid (1 species), mitochondrial (6 species) or chloroplast (8
 species) genomes. These species come from 19 different phyla, scattered
 across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA
 viral Rep tree topology suggested potential hosts for one family of
 uncharacterized viruses and supports a primarily fungal host range for
 genomoviruses.
description: The endogenous viral sequences were extracted directly
 from tBLASTn results, which are amino acid sequences translated from
 nucleotide sequences, GenBank accession and genomic coordinates are
 available in the corresponding label files(.txt) and supplement table of
 the manuscript.  The endogenous viral sequences were
 combined with viral query sequences used to generate them, and aligned
 using MUSCLE and trimmed by TrimAl (detail in Method section of
 manuscript). Phylogenetic trees were built with the
 aligned and trimmed alignments using PhyML 3.0, using CRESS+G+F
 model. The trees can be viewed using FigTree and label
 files can be imported using FigTrees' "import annotation"
 option. The CRESS model is also provided here. The
 derivation of the CRESS model is available
 here: doi: https://doi.org/10.1101/687855
DOI: 10.5061/dryad.c59zw3r7z
title: Practical guide to using Kendall’s τ in the context of forecasting critical transitions

description: Recent studies demonstrate that trends in indicators extracted from
 measured time series can indicate approaching to an impending transition.
 Kendall’s τ coefficient is often used to study the trend of statistics
 related to the critical slowing down phenomenon and other methods to
 forecast critical transitions. Because statistics are estimated from time
 series, the values of Kendall’sτare affected by parameters such as window
 size, sample rate and length of the time series, resulting in challenges
 and uncertainties in interpreting results. In this study, we examine the
 effects of different parameters on the distribution of the trend obtained
 from Kendall’s τ, and provide insights into how to choose these
 parameters. We also suggest the use of the non-parametric Mann-Kendall
 test to evaluate the significance of a Kendall’sτvalue. The non-parametric
 test is computationally much faster compared to the traditional parametric
 ARMA test.
DOI: 10.5061/dryad.zcrjdfncs
title: Data for: Warm night temperature alters paternal allocation strategy in a North temperate zone butterfly

description: Warming temperatures are greatly impacting wild organisms across the
 globe. Some of the negative impacts of climate change can be mitigated
 behaviorally, for example, by changes in habitat and oviposition site
 choice. Temperatures are reportedly warming faster at night than during
 the day, yet studies assessing the impacts of increasing night temperature
 are rare. We used the Finnish Glanville fritillary butterfly (Melitaea
 cinxia) as study species and exposed adult butterflies of both sexes to
 warmer night conditions. Under a semi-natural outdoor enclosure, we
 assessed whether females base their oviposition choices primarily on
 habitat site characteristics (open, suggestive of dry meadows vs covered
 by a coarse canopy,  suggestive of pastures) or on plant
 condition (dry vs lush), and if their choice is altered by the thermal
 conditions experienced at night.  As exposure to warmer
 environmental conditions is expected to increase resting metabolic rate
 and potentially reduce life expectancy, we further assessed the fitness
 implications of warm night temperatures. We found that females prefer open
 sites for oviposition and that females do not switch their oviposition
 strategy based on the thermal conditions they experienced at night prior
 to the reproductive event. Exposure to warm nights did not influence
 female lifespan, but the egg hatching success of their offspring was
 reduced. In addition, we found that males exposed to warm nights sired
 larger clutches with higher hatching rate. As warm night exposure reduced
 male lifespan, this may imply a switch in male resource allocation
 strategy towards increased offspring quality. The present work adds on to
 the complex implications of climate warming and highlights the importance
 of the often-neglected role of males in shaping offspring performance.
DOI: 10.5061/dryad.f7m0cfxx6
title: Spatial and temporal variation in phenotypes and fitness in response to developmental thermal environments

description: 1) Phenotypic variation within populations is influenced by the
 environment via plasticity and natural selection. How phenotypes respond
 to the environment can vary among traits, populations, and life stages in
 ways that can influence fitness. 2) Plastic responses during early
 development are particularly important because they can affect components
 of fitness throughout an individual’s life. Consequently, how natural
 selection shapes developmental plasticity could be influenced by fitness
 consequences across different life stages. Moreover, spatial variation in
 selection pressures could generate differences in plastic responses among
 populations. 3) To gain insight into sources of variation in phenotypes
 and survival, we used a laboratory egg incubation experiment using brown
 anole lizards (Anolis sagrei) from mainland (ancestral) and island
 (descendent) populations, combined with a mark-release-recapture
 experiment in the field. Our study was designed to (i) quantify the
 effects developmental temperature on embryo development and offspring
 morphology, (ii) assess how developmental temperature influences offspring
 survival across different life stages, and (iii) quantify how thermal
 reaction norms vary among ancestral and descendant populations. 4)
 Developmental temperature influenced offspring morphology, but thermal
 reaction norms of embryos showed little variation among populations.
 Developmental temperature influenced offspring survival, but the patterns
 differed between embryo and hatchling stages; the optimal temperature for
 embryos was about 5ºC lower than that for hatchlings. High temperatures
 were thermally stressful to embryos, but they reduced incubation duration
 and led to early hatching. In turn, earlier hatching increased the
 probability of survival to adulthood. Moreover, the effect of temperature
 on hatchling survival was most pronounced for offspring that hatched late
 in the season. 5) The difference in optimal developmental temperatures
 between life stages may be driven by physiological tolerance for embryos
 and by ecological factors for hatchlings. Moreover, the fitness
 consequences of the developmental environment depend upon the phenology of
 hatching. Overall, these results highlight how the developmental
 environment can differentially effect fitness across life stages and show
 that temporal thermal heterogeneity can influence survival of embryos, but
 the consequences on post-hatching stages may vary at different times of
 the season.
DOI: 10.5061/dryad.4f4qrfjcv
title: Flash intensity and duration

description: These data were obtained by having individuals participate in a series of
 16-day studies, each with a 34-hour in-laboratory period. In this
 between-subjects design, we examined phase shifting in response to
 variable-intensity (3-9500 photopic lux) flashes at fixed duration (2 ms;
 n=28 participants) and variable-duration (10 μs-10 s) flashes at fixed
 intensity (2000 photopic lux; n=31 participants) for 1 hour with 15 s
 between flashes . Acute melatonin suppression, objective alertness, and
 subjective sleepiness during the flash sequence were also
 assessed. 
description: Melatonin phase shifting data were obtained during constant
 routine. Saliva samples were collected and later assessed for melatonin
 concentrations with a commercially-available ELISA (Salimetrics) based on
 a monoclonal melatonin antibody. Melatonin suppression,
 objective alertness (median reaction time on an auditory psychomotor
 vigilance test), and subjective sleepiness data (Stanford Sleepiness
 Scale) were obtained immediately before and after a 1-hour light
 exposure. 
description: See ReadMe file for usage notes
DOI: 10.5061/dryad.z08kprrdb
title: Data and code from: Fruit bat migration matches green wave in seasonal landscapes

description: Migrating grazers and carnivores respond to seasonal
 changes in the environment and often match peaks in resource abundance.
 However, it is unclear if and how frugivorous animals use phenological
 events to time migration, especially in the tropics. The
 straw-colored fruit bat (Eidolon helvum), Africa’s most gregarious fruit
 bat, forms large seasonal colonies throughout much of sub-Saharan Africa.
 We hypothesized that aggregations of E. helvum match the
 timing of their migration with phenologies of plant growth or
 precipitation. Using monthly colony counts from across much of
 the species’ range, we matched peak colony size to landscape phenologies
 and explored the variation among colonies matching the overall closest
 phenological event. Peak colony size was closest
 to the peak instantaneous rate of
 green-up, and sites with closer temporal matching were associated
 with higher maximum greenness, short growing season, and larger peak
 colony size. Eidolon helvum seem to time their
 migrations to move into highly seasonal landscapes to exploit short-lived
 explosions of food and may benefit from collective sensing to time
 migrations. The link between rapid changes in colony size and
 phenological match may also imply potential collective sensing of the
 environment. Overall decreasing bat numbers along with various
 threats might cause this property of large colonies to be
 lost. Remote sensing data, although, indirectly linked to
 fruiting events, can potentially be used to globally describe and
 predict the migration of frugivorous species in a changing world.
description: Colonies of <em>Eidolon helvum</em> bats were counted
 by members of the Eidolon Monitoring Network (www.eidolonmonitoring.com)
 at seventeen sites across Africa. Most colonies were counted by observing
 the bats at their roost site and multiplying the average number of bats in
 a cluster, the average number of clusters on a branch, the average number
 of occupied branches in a tree, and the number of occupied trees at the
 roost site (Hayman et al. 2012; Fahr et al. 2015). For roosts that were inaccessible without disturbing the colony, observers would count numbers of passing bats during evening emergence and extrapolate their numbers by the area monitored (Sørensen & Halberg 2001). The table includes the longitude and latitude coordinates of the roost, geeID (a unique ID for each location use to extract remote sensing values from Google Earth Engine), country, location (city or park), date of the count, count estimate, and observer names. We calculated the ratio of the colony size as the fraction of the maximum colony size for that site across a moving window of all counts within a year, before and after each count.
description: See the attached ReadMe file and see https://github.com/ehurme/EidolonGreenWave and www.eidolonmonitoring.com for the latest updates to the code and counts.
DOI: 10.5061/dryad.573n5tb87
title: Building better conservation media for primates and people: A case study of orangutan rescue and rehabilitation YouTube videos

description: 1. Conservation organizations rely on social/internet media platforms to
 raise awareness and fundraise. Social media is a double-edged sword: it
 can be a wide-reaching and effective tool for education and fundraising,
 but can also have counter-productive impacts on public views toward
 wildlife and understanding of wildlife conservation. 2. For example,
 depicting humans interacting with wildlife in media may increase video
 popularity, but animals shown in anthropogenic contexts are also viewed as
 appealing pets. We are interested in understanding whether this is true
 for social media posts (YouTube videos) by orangutan rescue and
 rehabilitation organizations, which rely on social media for fundraising
 and awareness-raising. Our goal is to provide data and recommendations to
 guide these organizations in building media with positive conservation
 impact while minimizing potential negative effects. 3. Using YouTube
 analytics and sentiment analysis of comments on 118 videos, we ask how
 viewer responses to videos vary with 1) the amount of human-orangutan
 interaction depicted, 2) the ages of the orangutans featured, and 3) the
 mention of threats to orangutans. 4. Videos with longer human-orangutan
 interaction time were viewed more, but comments on them were significantly
 more likely to be negative toward Indonesian/Malaysian people. Comments on
 orangutan rescue/rehabilitation videos were more likely to be categorized
 as negative for orangutan conservation compared to videos about orangutans
 generally, and within these, so were comments on videos featuring infant
 and juvenile orangutans. 5. Based on our findings, we recommend that
 orangutan rescue and rehabilitation organizations feature adult and mixed
 age groups of orangutans rather than infants and juveniles, minimize the
 amount of human-orangutan interaction shown, and talk about conservation
 threats to orangutans in their videos. We also recommend that, as a
 precaution, other primate rescue and rehabilitation groups also abide by
 these suggestions.
description: Data were collected from 118 Youtube videos according to methods
 described in detail in the manuscript.
description: Video metrics (likes, dislikes, and comments) were standardized
 to the number of views in the dataset. The human-orangutan interaction
 time for each video was also standardized, to the video length. In all
 cases, the result is a ratio ranging from 0-1. This is described in the
 manuscript.
DOI: 10.5061/dryad.np5hqbztn
title: Abiotic factors influence species co‐occurrence patterns of lake fishes

description: This dataset contains the identity of the lakes used for the analyses
 performed in the paper: Cordero, R., & Jackson, D. (2021). Abiotic
 factors influence species co‐occurrence patterns of lake
 fishes. Journal of Animal Ecology. doi:10.1111/1365-2656.13587”.
 This study analyzed the effect of habitat size (i.e., lake area and depth)
 on the pattern of co-occurrence of multiple fish species in lakes from two
 different regions, western and central, in Ontario, Canada. The main
 results of this study were that area and depth showed a significant
 influence across all the species co-occurrence patterns, in both regions.
 However, when analyzing groups of species involved in biotic interactions
 like predator-prey or species sharing similar habitat requirements, we
 found significant results only for lake area in the central region, which
 suggests a context-dependency on factors linked with region. Our results
 demonstrate the effect of environmental variables on species co-occurrence
 patterns, but the divergent results obtained between geographic regions
 suggest that such patterns are context-dependent. This study emphasizes
 the importance of considering abiotic factors in null models of species
 co-occurrence to obtain reliable and detailed information about the
 association patterns between species.
description: We used data from the Aquatic Habitat Inventory (AHI), which is a
 program from the Ontario Ministry of Natural Resources and Fisheries, and
 it was conducted from 1968 to 1985 having regular updating with data
 collected by new studies. This database contains records of the
 presence-absence of 99 fish species, including introduced species, in
 almost 9900 lakes (sampling units) distributed across Ontario.
 The AHI program was designed to sample all fish habitats within
 each lake using a variety of gill nets, seine nets, minnow traps, and
 electrofishing devices and provides species presence-absence data along
 with select environmental data. Here, we show only the identity and
 location of the subset of analyzed lakes in this study.
 From the database of the Aquatic Habitat Inventory (AHI) which is
 a program created by the Ontario Ministry of Natural Resources and
 Forestry, we grouped several tertiary watersheds from the central and
 northwestern regions in Ontario based on adjacency of watersheds and
 similarity of community composition. This approach allowed us to gather a
 greater number of lakes into a common set within each of the two regions
 considered while controlling for biogeographical influences (e.g.,
 post-glacial colonization, climate). We analyzed a total of 1102 lakes,
 grouped in three adjacent tertiary watersheds in the central region of
 Ontario, and 1238 lakes grouped in 6 adjacent tertiary watersheds in the
 northwestern region of Ontario.
description: This database contains the identity and location (latitude and
 longitude) of each lake analyzed.
DOI: 10.5061/dryad.79cnp5hw7
title: Distinct type II opsins in the eye decode light properties for background adaptation and behavioural background preference

description: Crypsis increases survival by reducing predator detection. Xenopus laevis
 tadpoles decode light properties from the substrate to induce two
 responses: A cryptic coloration response where dorsal skin pigmentation is
 adjusted to the colour of the substrate (background adaptation) and a
 behavioural crypsis where organisms move to align with a specific colour
 surface (background preference). Both processes require organisms to
 detect reflected light from the substrate. We explored the relationship
 between background adaptation and preference and the light properties able
 to trigger both responses. We also analysed which retinal photosensor
 (type II opsin) is involved. Our results showed that these two processes
 are segregated mechanistically, as there is no correlation between the
 preference for a specific background with the level of skin pigmentation,
 and different dorsal retina-localized type II opsins appear to underlie
 the two crypsis modes. Indeed, inhibition of melanopsin affects background
 adaptation but not background preference. Instead, we propose pinopsin is
 the photosensor involved in background preference. pinopsin mRNA is
 co-expressed with mRNA for the sws1 cone photopigment in dorsally-located
 photoreceptors. Importantly, the developmental onset of pinopsin
 expression aligns with the emergence of the preference for a white
 background, but after the background adaptation phenotype appears.
 Furthermore, white background preference of tadpoles is associated with
 increased pinopsin expression, a feature that is lost in pre-metamorphic
 froglets along with a preference for a white background. Thus, our data
 show a mechanistic dissociation between background adaptation and
 background preference, and we suggest melanopsin and pinopsin,
 respectively, initiate the two responses.
description: Physiological skin pigmentation indices were measured as
 described previously (Bertolesi et al 2015). Briefly, pictures of the
 dorsal head of tadpoles were taken with identical conditions of light,
 time exposure and diaphragm aperture, and converted to binary white/black
 images using NIH ImageJ (U. S. National Institutes of Health, Bethesda,
 MD) public domain software. Behaviour assay of embryos
 was performed as described previously (Viczian & Zuber,
 2014). Briefly, a minimum of nine embryos were tested simultaneously, each
 in individual boxes (6.5 x 9.0 x 2.5 cm) set over a platform with light
 from above (1200 lux) in a quiet room. Embryos were recorded using a
 Logitech C920S camera. Each individual box was divided into equal half
 area white and black surfaces, and each embryo was recorded for 7-10
 cycles of 2 min each (total 840-1200 sec).
DOI: 10.15468/dl.6e84gs
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((137.70647 36.73772,137.56396 36.64076,137.58495 36.47634,137.74442 36.41806,137.8389 36.45856,137.84592 36.60317,137.82434 36.70716,137.70647 36.73772))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pinus pumila"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002928-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m905qfv1s
title: A new faunistic component of the Lower Triassic Panchet Formation of India increases the continental non-archosauromorph neodiapsid record in the aftermath of the end-Permian mass extinction

description: The fossil record of Early Triassic diapsids is very important to
 understand how the end-Permian mass extinction affected ecosystems and the
 patterns and processes involved in the subsequent biotic recovery.
 Vertebrate fossil assemblages of continental deposits in current-day South
 Africa, China and Russia are the best source of information of this clade
 during the aftermath of the extinction event. Although considerably less
 sampled, the Induan continental rocks of the Panchet Formation of the
 Damodar Basin (eastern India) have also yielded a relatively diverse
 vertebrate assemblage composed of fishes, temnospondyls, synapsids, and a
 single proterosuchid taxon. Here, we report on a small isolated diapsid
 partial ilium (ISIR 1132) from the upper Panchet Formation. This specimen
 has a distinct morphology to that present in other tetrapods that we are
 aware of, including a shallow emargination on the dorsal margin of the
 anterior portion of the iliac blade, and ratio between height of iliac
 blade versus maximum height of iliac acetabulum at level of the dorsalmost
 extension of supraacetabular crest ≤0.45. Comparisons and a quantitative
 phylogenetic analysis found ISIR 1132 as a non-archosauromorph neodiapsid.
 This new specimen expands the reptile diversity in the Panchet Formation
 as well as for the rest of Gondwana, where Early Triassic
 non-archosauromorph neodiapsid species are extremely scarce.