cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.88d5v17
title: Data from: The cryptic regulation of diversity by functionally complementary large tropical forest herbivores

description: 1. Tropical forests hold some of the world’s most diverse communities of
 plants. Many populations of large-bodied herbivores are threatened in
 these systems, yet their ecological functions and contribution towards the
 maintenance of high levels of plant diversity are poorly known. The impact
 of these herbivores on plant communities through antagonistic seed and
 seedling predation has received much attention, whilst their relevance as
 seed dispersal agents has been largely overlooked in experimental studies.
 2. Here we tested how two key and functionally distinct large generalist
 mammalian herbivore species (the tapir Tapirus terrestris- a solitary
 browser and generalist seed disperser, and the white-lipped peccary
 Tayassu pecari- a group-living generalist seed/seedling predator) affect
 spatiotemporal patterns of diversity of seedling communities in tropical
 forests. We conducted a long-term multi-region landscape-scale exclusion
 experiment across four regions of the Atlantic forest of Brazil,
 representing a functional gradient of defaunation where these species were
 either present and absent in isolation and in combination. 3. Our results
 indicate that mammalian herbivores have a substantial role in regulating
 beta diversity in space and time. Seedling recruitment was strongly
 limited by the presence of the seed/seedling predator species (the
 peccary), but the presence of the browser and seed disperser (the tapir)
 had null net effects. Alpha diversity of seedlings at the community level
 did not respond to large herbivore exclusion at any region, whereas beta
 diversity decreased only where both herbivores were simultaneously
 excluded. Surprisingly, the synergic positive effect of both herbivore
 types on beta diversity was linked to increased evenness amongst dominant
 plant species, and a simultaneous decrease in alpha diversity of rare
 species. 4. Synthesis: Together, these results challenge the common
 perception that large tropical forest herbivores maintain tropical forest
 diversity through antagonistic interactions, suggesting instead a
 synergistic effect of antagonistic predation and mutualistic seed
 dispersal on regional compositional diversity and local community
 assembly. We suggest that the defaunation of large-bodied herbivores with
 complementary functions strongly affects the structure and dynamics of
 plant communities through cryptic mechanisms that remain largely
 unexplored.
description: Villar_et_al_JoEco2019_dataDatasets used to estimate the effects of defaunation from functionally distinct large herbivores on the spatiotemporal structure of seedling communities in the Atlantic Forest of Brazil
DOI: 10.5061/dryad.cv1jg30
title: Data from: Seasonal drivers of understorey temperature buffering in temperate deciduous forests across Europe

description: Aim: Forest understory microclimates are often buffered against extreme
 heat or cold, with important implications for the organisms living in
 these environments. We quantified seasonal effects of understory
 microclimate predictors describing canopy structure, canopy composition
 and topography (i.e. local factors), as well as forest patch size and
 distance to coast (i.e. landscape factors). Location: Temperate forests in
 Europe Time period: 2017-2018 Major taxa studied: Woody plants Methods: We
 combined data from a microclimate sensor network with weather station
 records to calculate the difference – or offset – between temperatures
 measured inside and outside forests. We used regression analysis to study
 the effects of local and landscape factors on the seasonal offset of
 minimum, mean and maximum temperatures. Results: Maximum temperature
 during summer was on average cooler by 2.1 °C and minimum temperature
 during winter and spring were 0.4 °C and 0.9 °C warmer inside than outside
 forests. The local canopy cover was a strong non-linear driver of the
 maximum temperature offset during summer, and we found increased cooling
 beneath tree species that cast the deepest shade. Seasonal offsets of
 minimum temperature were mainly regulated by landscape and topographic
 features, such as the distance to coast and topographic position. Main
 conclusions: Forest organisms experience less severe temperature extremes
 than suggested by currently available macroclimate data, so
 climate-species relationships and species’ responses to anthropogenic
 global warming cannot be modelled accurately in forests using macroclimate
 data alone. Changes in canopy cover and composition will strongly modulate
 warming of maximum temperatures in forest understories, with important
 implications for understanding responses of forest biodiversity and
 functioning to the combined threats of land-use change and climate change.
 Our predictive models are generally applicable across lowland temperate
 deciduous forests, providing ecologically important microclimate data for
 forest understories.
description: Data used in Zellweger
 et al. 2019 GEBdata.csv
DOI: 10.5061/dryad.dj343ht
title: Data from: Benefits of increased colonist quantity and genetic diversity for colonization depend on colonist identity

description: Larger numbers of colonists can be more likely to establish and spread due
 to the benefits provided by either more individuals (quantity) or a
 greater diversity of genotypes or phenotypes (genetic diversity). However,
 the value of higher colonist quantity or genetic diversity varies widely
 across studies, leaving a great deal of uncertainty in how these
 respective mechanisms affect colonization success. This variability is
 potentially driven by differences in which traits are present in
 respective colonist pools (‘colonist identity’). Studies with
 high-performing colonizers (e.g. genotypes pre-adapted to the colonizing
 environment) may find increasing quantity or diversity to be beneficial
 because it increases the chance high-performers are sampled, while studies
 with no high-performers may find no effects of quantity or diversity.
 Alternatively, quantity and genetic diversity may play little to no role
 if the smallest populations already contain high-performing colonists
 because there is no scope for a sampling effect to operate. We conducted a
 field mesocosm experiment to determine if variability in the benefits
 provided by increased quantity or genetic diversity relates to colonist
 traits. Nine distinct genotypes of Daphnia pulex, characterized also by
 phenotype, were introduced in ‘single’ (one individual) or ‘many’ (nine
 individuals) introduction quantities and at ‘low’ (monoclonal) and ‘high’
 (mixed genotypes) genetic diversities. We found that larger-bodied D.
 pulex genotypes benefited less from increased colonist quantity, while
 increasing genetic diversity tended to have a lower effect on higher
 growth rate genotypes. Our results show that the trait values of the
 colonists can determine the benefits gained when colonist quantity or
 genetic diversity are increased, with potential applications to future
 research and practical efforts to promote, or prevent, population
 establishment.
description: Daphnia pulex density
 long-form data for all replicates in all treatmentsThe nine experimental
 genotypes are denoted by their respective letter identifiers under the
 heading 'genotype', along with the 'Mixed' genotype
 treatment. The single (1 colonist) or many (9 colonists) quantity
 treatment is denoted under the 'quantity' heading. The
 'replicate' heading identifies the individual replicates in each
 treatment (n=6 for single treatments, n=5 for many treatments, n=5 for the
 Mixed treatment). The density (individuals per L) values plotted in Figure
 1 and used to calculate treatment effect sizes are given in the
 'density(ind/L)' column.Sinclairetal - Benefits of
 increased colonist quantity and genetic diversity for colonization depend
 on colonist identity.csv
DOI: 10.34943/3b10ca0e-e74f-414e-a727-5e2accafc254
title: Mantis Navigation System Deployed 2024-10-04

description: The Mantis ROV Navigation 01 was deployed on 2024-10-04 on Mantis. This Remotely Operated Vehicle is operated by CanPac Marine Services Inc. This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/eceed5e7-3c07-45b4-8b26-c932b7d53550
title: Mantis Navigation System Deployed 2025-03-18

description: The Mantis ROV Navigation 01 was deployed on 2025-03-18 on Mantis. This Remotely Operated Vehicle is operated by CanPac Marine Services Inc. This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5061/dryad.814vb1b
title: Data from: The environmental predictors of spatiotemporal variation in the breeding phenology of a passerine bird

description: Establishing the cues or constraints that influence avian timing of
 breeding is key to accurate prediction of future phenology. This study
 aims to identify the aspects of the environment that predict the timing of
 two measures of breeding phenology (nest initiation and egg laying date)
 in an insectivorous woodland passerine, the blue tit (Cyanistes
 caeruleus). We analyse data collected from a 220km, 40-site transect over
 three years and consider spring temperatures, tree leafing phenology,
 invertebrate availability and photoperiod as predictors of breeding
 phenology. We find that mean night-time temperature in early spring is the
 strongest predictor of both nest initiation and lay date and suggest this
 finding is most consistent with temperature acting as a constraint on
 breeding activity. Birch budburst phenology significantly predicts lay
 date additionally to temperature, either as a direct cue or indirectly via
 a correlated variable. We use cross-validation to show that our model
 accurately predicts lay date in two further years, and find that similar
 variables predict lay date well across the UK national nest record scheme.
 This work refines our understanding of the principal factors influencing
 the timing of tit reproductive phenology, and suggests that temperature
 may have both a direct and indirect effect.
description: Shutt_Phillimore_ProcB_DataContaining blue tit phenology data from a Scottish transect, along with measures of putative predictors of phenology (temperature, tree phenology, invertebrate abundance and latitude).
DOI: 10.34943/425025e6-0f66-4db4-a5ca-2de1bea27131
title: Mantis Navigation System Deployed 2025-05-25

description: The Mantis ROV Navigation 01 was deployed on 2025-05-25 on Mantis. This Remotely Operated Vehicle is operated by CanPac Marine Services Inc. This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5061/dryad.70v5js4
title: Data from: Consistent female preference for rare and unfamiliar male color patterns in wild guppy populations

description: How genetic variation is maintained in ecologically important traits is a
 central question in evolutionary biology. Male Trinidadian guppies,
 Poecilia reticulata, exhibit high genetic variation in color patterns
 within populations, and field and laboratory studies implicate negative
 frequency-dependent selection in maintaining this variation. However,
 behavioral and ecological processes that mediate this selection in natural
 populations are poorly understood. We evaluated female mate preference in
 11 natural guppy populations, including paired populations from high-and
 low-predation habitats, to determine if this behavior is responsible for
 negative frequency-dependent selection and to evaluate its prevalence in
 nature. Females directed significantly more attention to males with rare
 and unfamiliar color patterns than to males with common patterns. Female
 attention also increased with the area of male orange coloration, but this
 preference was independent of the preference for rare and unfamiliar
 patterns. We also found an overall effect of predation regime; females
 from high-predation populations directed more attention toward males than
 those from low-predation populations. Again, however, the habitat-linked
 preference was statistically independent from the preference for rare and
 unfamiliar patterns. Because previous research indicates that female
 attention to males predicts male mating success, we conclude that the
 prevalence of female preference for males with rare and unfamiliar color
 patterns across many natural populations supports the hypothesis that
 female preference is an important process underlying the maintenance of
 high genetic variation in guppy color patterns.
description: Guppy_MasterData file containing variables used in the analysis
DOI: 10.34943/245f35cd-69b1-47fb-96ce-fd63a8cb961b
title: Mantis Navigation System Deployed 2025-09-04

description: The Mantis ROV Navigation 01 was deployed on 2025-09-04 on Mantis. This Remotely Operated Vehicle is operated by CanPac Marine Services Inc. This device is a Navigation System. Navigational instruments are used to measure and record positional information of ships, buoys, and autonomous underwater vehicles (AUVs). Typical sensors include latitude, longitude, speed, heading, pitch, roll, and depth. It was deployed on a mobile platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5061/dryad.v8kj429
title: Data from: Climate change, snow mold, and the Bromus tectorum invasion: mixed evidence for release from cold weather pathogens

description: Climate change is reducing the depth and duration of winter snowpack,
 leading to dramatic changes in the soil environment with potentially
 important ecological consequences. Previous experiments in the
 Intermountain West of North America indicated that loss of snowpack
 increases survival and population growth rates of the invasive annual
 grass Bromus tectorum; however, the underlying mechanism is unknown. We
 hypothesized that reduced snowpack might promote B. tectorum population
 growth by decreasing damage from snow molds, a group of subnivean fungal
 pathogens. To test this hypothesis, we conducted greenhouse and field
 experiments to investigate the interaction between early snowmelt and
 either fungicide addition or snow mold infection of B. tectorum. The
 greenhouse experiment confirmed that the snow mold Microdochium nivale can
 cause mortality of B. tectorum seedlings. In the field experiment, early
 snowmelt and fungicide application both increased B. tectorum survival,
 but their effects did not interact, and snow mold inoculation had no
 effect on survival. We did find interactive effects of snowmelt and fungal
 treatments on B. tectorum seed production: with ambient snowpack, M.
 nivale inoculation reduced seed production and fungicide increased it,
 whereas in the early snowmelt treatment seed production was high
 regardless of fungal treatment. However, treatment effects on seed
 production did not translate directly to overall population growth, which
 did not respond to the snow melt by fungal treatment interaction. Based on
 our mixed results, the hypothesis that reduced snowpack may increase B.
 tectorum fitness by limiting the effects of plant pathogens deserves
 further investigation.
description: Data and
 codeThe zip archive contains
 all the data files and R code needed to reproduce the analyses in the
 published paper. It also contains a readme file and a metadata
 file.datapluscode.zip
DOI: 10.5061/dryad.c5g4qt7
title: Data from: Anthropogenic disturbance and rainfall variation threaten the stability of plant‐ant interactions in the Brazilian Caatinga

description: Climate change is projected to exacerbate the effects of anthropogenic
 disturbance, with negative impacts on ecosystem stability and functioning.
 We evaluate the additive and combined effects of chronic anthropogenic
 disturbance (CAD) and rainfall variation on the temporal stability of
 mutualistic EFN‐bearing plant‐ant networks in a Caatinga dry forest. We
 evaluated whether changes in the stability of these interactions are
 driven by changes in the stability of the communities of partners involved
 and/or in ant behavior. We sampled EFN‐bearing plant‐ant networks in
 sixteen 20m×20m plots distributed across CAD and rainfall gradients. The
 stability of EFN‐bearing plant and attendant‐ant communities were measured
 as the inverse of temporal differences in their community structure and
 composition. We also computed the stability of EFN‐bearing plant‐ant
 networks by measuring the inverse of temporal differences in network
 specialization metrics. We found that, in general, the structure and
 composition of plant and ant interacting communities were similarly stable
 along both environmental gradients. Only CAD and its interaction with
 rainfall affected the temporal stability of EFN‐bearing plant diversity,
 which declined as CAD increased, with a more pronounced relationship in
 wetter areas. However, variation in levels of CAD and, to a lesser extent,
 rainfall greatly modulated the stability of EFN‐bearing plant‐ant network
 specialization. CAD reduced the stability of network generality
 (specialization at the ant level), an effect that was much stronger in
 wetter areas. Meanwhile, the stability in network vulnerability
 (specialization at the plant level) decreased with the increase of CAD and
 the decrease of rainfall levels. Finally, there was a trend of decreasing
 stability in specialization of the overall network with increasing CAD.
 Our results suggest that changes in the structure of interaction networks
 are mainly driven by a switch in ant behavior rather than by changes in
 the structure and composition of plant and ant communities between years.
description: Ant-plant
 surveySurvey of ant-plant
 interactions during 2014 and 2016 along CAD and rainfall gradients in a
 Seasonally Dry Tropical Forest in BrazilCamaraetal_2019_Ecography_dryad.xlsx
DOI: 10.5061/dryad.0nj71g0
title: Data from: More than skin and bones: comparing extraction methods and alternative sources of DNA from avian museum specimens

description: Next-generation sequencing has greatly expanded the utility and value of
 museum collections by revealing specimens as genomic resources. As the
 field of museum genomics grows, so does the need for extraction methods
 that maximize DNA yields. For avian museum specimens, the established
 method of extracting DNA from toe pads works well for most specimens.
 However, for some specimens, especially those of birds that are very small
 or very large, toe pads can be a poor source of DNA. In this study, we
 apply two DNA extraction methods (phenol-chloroform and silica column) to
 three different sources of DNA (toe pad, skin punch, and bone) from ten
 historical avian museum specimens. We show that a modified
 phenol-chloroform protocol yielded significantly more DNA than a silica
 column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across
 all tissue types. However, extractions using the silica column protocol
 contained longer fragments on average than those using the
 phenol-chloroform protocol, likely a result of loss of small fragments
 through the silica column. While toe pads yielded more DNA than skin
 punches and bone fragments, skin punches proved to be a reliable
 alternative source of DNA and might be especially appealing when toe pad
 extractions are impractical. Overall, we found that historical bird museum
 specimens contain substantial amounts of DNA for genomic studies under
 most extraction scenarios, but that a phenol-chloroform protocol
 consistently provides the high quantities of DNA required for most current
 genomic protocols.
description: Phenol-chloroform
 extraction of DNA from avian museum specimensA comprehensive
 phenol-chloroform protocol for extracting DNA from avian museum specimens.
 The protocol includes steps for tissue collection of toe pads, skin
 punches, and bones, and a step-by-step guide to the extraction protocol
 and a high ratio bead clean intended to maintain all fragments while
 removing impurities and PCR inhibitors.phenol-chloroform-extraction-protocol.pdf
DOI: 10.5061/dryad.nv89424
title: Data from: Cope’s Rule in a modular organism: directional evolution without an overarching macroevolutionary trend

description: Cope’s Rule describes increasing body size in evolutionary lineages
 through geological time. This pattern has been documented in unitary
 organisms but does it also apply to module size in colonial organisms? We
 address this using 1169 cheilostome bryozoans ranging through the entire
 150 million years of their evolutionary history. The temporal pattern
 evident in cheilostomes as a whole shows no overall change in zooid
 (module) size. However, individual subclades show size increases: within a
 genus, younger species often have larger zooids than older species.
 Analyses of (paleo)latitudinal shifts show that this pattern cannot be
 explained by latitudinal effects (Bergmann’s Rule) coupled with younger
 species occupying higher latitudes than older species (an ‘out of the
 tropics’ hypothesis). While it is plausible that size increase was linked
 to the advantages of large zooids in feeding, competition for trophic
 resources and living space, other proposed mechanisms for Cope’s Rule in
 unitary organisms are either inapplicable to cheilostome zooid size or
 cannot be easily evaluated. Patterns and mechanisms in colonial organisms
 cannot and should not be extrapolated from the better-studied unitary
 organisms. And even if macroevolution simply comprises repeated rounds of
 microevolution, evolutionary processes occurring with lineages are not
 always detectable from macroevolutionary patterns.
description: Zooid Size
 DataZooid (Module) size data
 used in the paper. Age span from late Jurassic to the Recent. Unique
 cheilostome species traceable to Paul D. Taylor's Scanning Electron
 Micrograph (SEM) collection deposited at the Natural History Museum,
 LondonZooid.size.over.time.final.csvNew Zealand Pleistocene cheilostome species zooid size dataThese data are from our previous publication (Liow L.H., Di Martino E., Krzeminska M, Ramsfjell M, Rust S., Taylor P.D. & Voje K.L. Relative size predicts competitive outcome through 2 million years. Ecology Letters 20: 981–988) but are needed to plot SI figure 1MK_size_data.csvGeologic StagesData file needed by R code to make some of the plots. These are standard geologic stagesFormations.csvR code for Cope's Rule in cheilostomesThis text file is the full R code for reading, analyzing and plotting the main text files and SI files and generating the results accompanying the publication "Cope’s Rule in a modular organism: Directional evolution without an overarching macroevolutionary trend" by Liow, Lee Hsiang and Taylor, Paul D. Note that some of the code are redundant.Zooid.size.code.2.7.2019.R