cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbccbk
title: Data: Direct and indirect effects of high temperatures on fledging in a cooperatively breeding bird

description: High temperatures and low rainfall consistently constrain reproduction in
 arid-zone bird species. Understanding the mechanisms underlying this
 pattern is critical for predicting how climate change will influence
 population persistence and to inform conservation and management. In this
 study, we analysed Southern Pied Babbler Turdoides bicolor nestling
 survival, daily growth rate and adult investment behaviour during the
 nestling period over three austral summer breeding seasons. High
 temperatures were associated with lower body mass, shorter tarsi, and
 reduced daily growth rates of nestlings. Our piecewise structural equation
 models suggested that direct impacts of temperature had the strongest
 influence on nestling size and daily growth rates for both 5-day-old and
 11-day-old nestlings, followed by temperature-related adjustments to
 provisioning rates by adults.  Rainfall and group size influenced
 the behaviour of provisioning adults but did not influence nestling growth
 or survival. Adjustments to adult provisioning strategies did not
 compensate for direct negative effects of high air temperatures on
 nestling size or daily growth rates. Detailed mechanistic data like these
 allow us to model the pathways by which high temperature causes nest
 failure. In turn, this could allow us to design targeted conservation
 action to effectively mitigate climate effects.
DOI: 10.25349/d9532w
title: The release of inertial instability near an idealized zonal jet

description: Inertial instability is a hydrodynamic instability that occurs in strong
 anticyclonic flow and is typically diagnosed by negative absolute
 vorticity in the Northern Hemisphere. As such, inertial instability is
 often observed on the anticyclonic-shear side of jet streams, yet the
 release of the instability in this environment is still poorly understood.
 We simulate the release of inertial instability near an idealized
 midlatitude zonal jet compared a control simulation with no instability.
 We find that the release of the instability results in flat meridional
 wind perturbations of up to 7 m/s over 200 km that persist for several
 days, in addition to radiating inertia-gravity waves several hundreds of
 kilometers away from the unstable region. Furthermore, these perturbations
 instigate light-moderate occurrences of clear-air turbulence around the
 unstable region that persist for up to 12 hours.
description: The model used in this study is Cloud Model 1 (CM1) version
 19.4.
DOI: 10.5061/dryad.9w0vt4bfv
title: Compendium of dengue cases from 2013 to 2017

description: Dataset with the occurrences of dengue cases from 2013 to 2017. The
 following information is provided: year, continent, country, admi 1
 (largest subnational administrative unit in the country), admi 2 (second
 largest subnational administrative unit in the country: province,
 district, municipality or canton), latitude, longitude, and
 location. The location indicates whether
 coordinates refer to precise localities or
 to polygon centroids. In the latter case, only
 polygons with around 7,774-km2-size area or less were
 considered.
DOI: 10.5061/dryad.t76hdr816
title: Data from: Discovery of proteinaceous moieties in Late Cretaceous dinosaur eggshells

description: The documentation of proteinaceous soft tissues in fossils from deep time
 remains controversial. Often this has been attributed to the laboratory or
 other modes of modern contamination. Here we provide incontrovertible
 evidence for the preservation of proteinaceous moieties in the
 Maastrichtian dinosaur eggshells using pyrolysis-GC×GC-TOFMS. The presence
 of nitrogen-bearing organic molecules along with diketodipyrrole suggest
 that the proteinaceous moieties can survive diagenesis. The preservation
 of these proteinaceous moieties has been attributed to deposition in a
 palustrine flat environment under subaerial conditions and entrapment of
 organic material by the eggshell calcitic units. The present study
 demonstrates that the preservation of nitrogen-bearing macromolecules in
 Mesozoic fossil remains is not impossible provided the depositional
 environments and diagenetic processes are propitious. The survival of
 nitrogen-bearing macromolecule in deep time under subaerial depositional
 settings will open a new avenue to the research on soft tissue
 preservation.
DOI: 10.5061/dryad.jm63xsjb3
title: Behavioural, morphological, and life history shifts during invasive spread

description: Invasive species are common around the world, but we still do not know
 which traits are most important for successfully establishing in new
 environments. Different stages of the invasion process, including
 transport, introduction, establishment, and spread, can act as selective
 filters for different combinations of phenotypic traits. Theoretical and
 empirical studies predict that invasive populations should have suites of
 behaviours that improve dispersal and spread, including higher boldness,
 dispersal propensity, and activity levels than native populations. In this
 study, we tested these predictions by comparing the morphology, life
 history, and behaviour of an invasive populations of redback spiders,
 Latrodectus hasselti, from Japan to a population of native spiders from
 Australia, with additional comparisons of another invasive population from
 New Zealand. We found that both a longer-established invasive New Zealand
 population and the more recently-established invasive Japanese population
 were more dispersive than the native Australian population. The Japanese
 invasive population showed elevated levels of sibling cannibalism relative
 to the native population, which may increase total reproductive success of
 females under food limitation. Japanese spiders were also less bold in
 response to a simulated predator threat compared to the native Australian
 population. In contrast to the prediction that invasive populations would
 show uniformly fast life history traits, the invasive Japanese population
 was more fecund, yet took longer to develop than the native population
 under laboratory conditions. Overall, our results show that invasive
 populations are phenotypically distinct from native populations, with some
 behavioural, life history, and morphological traits that would increase
 spread (dispersal tendency, high fecundity) and persistence (sibling
 cannibalism) in new habitats.
description: We collected the data at the University of Toronto Scarborough in
 laboratory conditions. These are the raw data and haven't been
 processed.
DOI: 10.5061/dryad.c59zw3r78
title: Heating Arrays Aboveground Biomass Data

description: Restoration in this era of climate change comes with a new challenge:
 anticipating how best to restore populations to persist under future
 climate conditions. Specifically, it remains unknown whether
 locally-adapted or warm-adapted seeds best promote native plant community
 restoration in the warmer conditions predicted in the future and whether
 local or warm-adapted soil microbial communities could mitigate plant
 responses to warming. This may be especially relevant for biomes spanning
 large climatic gradients, such as the North American tallgrass prairie.
 Here, we used a short-term mesocosm experiment to evaluate how seed
 provenances (Local Northern region, Non-Local Northern region, Non-Local
 Southern region) of 10 native tallgrass prairie plants (four forbs, two
 legumes, and four grasses) responded to warmer conditions predicted in the
 future and how soil microbial communities from those three regions
 influenced these responses. Warming and seed provenance affected plant
 community composition, and warming decreased plant diversity for all three
 seed provenances. Plant species varied in their individual responses to
 warming, and across species, we detected no consistent differences among
 the three provenances in terms of biomass response to warming and few
 strong effects of soil provenance. Our work provides evidence that
 warming, in part, may reduce plant diversity and affect restored prairie
 composition. Because the southern provenance did not consistently
 outperform others under warming and we found little support for the “local
 is best” paradigm currently dominating restoration practice, identifying
 appropriate seed provenances to promote restoration success both now and
 in future warmer environments may be challenging. Due to the idiosyncratic
 responses across species, we recommend that land managers compare seeds
 from different regions for each species to determine which seed provenance
 performs best under warming and in restoration for tallgrass prairies.
DOI: 10.5061/dryad.80gb5mkr1
title: The geographic distribution of rodent granivory and cheek pouches across North America

description: Seeds are an important food resource for many rodents.  One of
 the specializations that many granivorous rodents exhibit to increase
 their efficiency in harvesting seeds is cheek pouches.  However,
 many rodent species lack cheek pouches.  We propose that the
 presence or absence of cheek pouches is related to seed size and the
 productivity of the habitat where those rodents reside. 
 Location  North America – United States and Canada.
 Taxon  Granivorous rodents. We divided granivorous rodents into
 those species with and without cheek pouches. We then compiled a list of
 plant species (n = 389) that are known or suspected to be dispersed by
 these rodents via scatter hoarding the seeds in soil and compared the
 richness distributions of small (≤10 mm) and large seeds (&gt;10 mm)
 to the distributions of rodents with and without cheek pouches. 
 Large seeds are generally too large to fit into cheek pouches so they are
 usually carried one at a time with the incisors. Most rodents
 with cheek pouches live in the arid southwestern North America, whereas
 most rodents that lack cheek pouches live in the mesic southeastern North
 America. The richness distribution of rodents with cheek pouches was more
 similar to the richness distribution of small seeds, and the richness
 distribution of rodents that lack cheek pouches was more similar to the
 richness distribution of large seeds (nuts), although details of these
 distributions differed significantly.  The body mass of rodents
 with cheek pouches (mean = 59.5 g) was significantly less than the body
 mass of rodents that lack cheek pouches (592.6 g). Large rodents
 that lack cheek pouches live mostly in the more productive southeastern
 portion of North America where there are many trees that produce large
 nuts.  Small rodent with cheek pouches live mostly in the less
 productive southwestern portion of North America where there are many
 shrubs, forbs, and grasses that produce small seeds.
description: Data was enumerated by using program R to count the number of
 overlapping animal and plant species across 197 sites in the United States
 and Canada. Unmanipulated data can be found from the International Union
 for Conservation of Nature (IUCN 2019) and Vander Wall and Moore
 2016.   IUCN.
 (2019). The IUCN Red List of Threatened Species Version 2019-6.2. https://www.iucnredlist.org. Downloaded on January 17<sup>th</sup>, 2020. Vander Wall, S. B. & Moore, C.M.  (2016).  Interaction diversity of North American seed-dispersal mutualisms.  <i>Global Ecology and Biogeography</i> 25, 1377-1386.
DOI: 10.5061/dryad.mgqnk98zz
title: Caution is warranted when using animal space-use and movement to infer behavioral states

description: Background: Identifying the behavioral state for wild animals that can’t
 be directly observed is of growing interest to the ecological community.
 Advances in telemetry technology and statistical methodologies allow
 researchers to use space-use and movement metrics to infer the underlying,
 latent, behavioral state of an animal without direct observations. For
 example, researchers studying ungulate ecology have started using these
 methods to quantify behaviors related to mating strategies. However,
 little work has been done to determine if assumed behaviors inferred from
 movement and space-use patterns correspond to actual behaviors of
 individuals. Methods: Using a dataset with male and female white-tailed
 deer location data, we evaluated the ability of these two methods to
 correctly identify male-female interaction events (MFIEs). We identified
 MFIEs using the proximity of their locations in space as indicators of
 when mating could have occurred. We then tested the ability of utilization
 distributions (UDs) and hidden Markov models (HMMs) rendered with single
 sex location data to identify these events. Results: For white-tailed
 deer, male and female space-use and movement behavior did not vary
 consistently when with a potential mate. There was no evidence that a
 probability contour threshold based on UD volume applied to an
 individual’s UD could be used to identify MFIEs. Additionally, HMMs were
 unable to identify MFIEs, as single MFIEs were often split across multiple
 states and the primary state of each MFIE was not consistent across
 events. Conclusions: Caution is warranted when interpreting behavioral
 insights rendered from statistical models applied to location data,
 particularly when there is no form of validation data. For these models to
 detect latent behaviors, the individual needs to exhibit a consistently
 different type of space-use and movement when engaged in the behavior.
 Unvalidated assumptions about that relationship may lead to incorrect
 inference about mating strategies or other behaviors.
description: <strong>wtd_mf_interactions.RData</strong>
 Hidden Markov model state identification and utilization
 distribution values for male-female interaction events identified from
 collared white-tailed deer in Pennsylvania, USA, from 2013-2016. Guide to
 object name notation: HMM = hidden Markov model state, UD = utilzation
 distribution values, males = male white-tailed deer, females = female
 white-tailed deer, liberal = event identified using proximity,
 conservative = event identified using proximity and cohesion, rut = full
 rut period, rutseasons = rut split into early, peak, and late
 seasons.
DOI: 10.5061/dryad.ns1rn8psv
title: Forest cover and connectivity have pervasive effects on the maintenance of evolutionary distinct interactions in seed dispersal networks

description: Seed dispersal by animals is one of the most important ecological
 processes in tropical forests, entailing millions of years of evolutionary
 adaptations of plants and frugivorous animals forming networks of
 interactions that, ultimately, contribute to the resilience of such
 forests. We analyze 29 seed dispersal networks in the threatened Atlantic
 Forest biodiversity hotspot, with data on the frequency of feeding visits
 by birds to fruiting plants to answer: (1) which are the effects of forest
 cover and landscape connectivity on the maintenance of phylogenetic
 diversity (PD) of interacting birds and plants and the evolutionary
 distinctiveness of the interactions (EDi) between them; and (2) how EDi
 and plant/bird PD affects the robustness of the interaction networks? We
 found that forest cover positively influences both plant and bird PD and
 EDi. Landscape connectivity is an important predictor of bird PD, but not
 plant PD, suggesting that the spatial arrangement of forest remnants is
 essential for guaranteeing bird movement among forest fragments.
 Furthermore, interaction networks of areas with higher PD and EDi had
 great robustness to the simulated extinction of species, which underscore
 the importance of larger forest blocks for conserving evolutionary
 information and, consequently, the health and natural resistance of seed
 dispersal networks against environmental change.
description: This dataset contains 29 tables of weighted interaction network
 between plants (columns) and frugivore birds from the Brazilian Atlantic
 Forest used in the manuscript "Forest cover and connectivity have
 pervasive effects on the maintenance of evolutionary distinct interactions
 in seed dispersal networks" published in Oikos Journal.
DOI: 10.6078/d1zt54
title: Supplementary information for aquatic and blood-feeding Diptera

description: Aquatic Diptera are some of the most diverse and notable flies, impacting
 human health and providing ecosystem services. Despite the importance of
 aquatic Diptera, the evolution of aquatic life history and blood-feeding,
 are not sufficiently understood. Here, we examine the evolution of aquatic
 life histories and their associations with blood-feeding across Diptera.
 Aquatic and blood-feeding Diptera are phylogenetically conserved across
 the fly tree of life. We found evidence that the most recent common
 ancestor of Diptera likely had an aquatic life history. We discuss the
 rise of blood-feeding flies and specifically speculate on its relation to
 aquatic life history. Blood-feeding behaviors often occur in fly lineages
 that also have aquatic life histories, but not significantly. Evidence
 suggests that adaptations to larval aquatic life history were a precursor
 for flies expanding their diets to take blood meals.
description: We pooled together aquatic and blood feeding annotations from
 various peer-reviewed sources, such as Adler & Courtney 2019 and
 Wiegmann et al. 2011. More about the code
 here: https://github.com/ninapak256/aquatic-diptera.
description: Not all infraorder or superfamilies are labeled, and annotations
 were made for families (not based on the species from the tips) that
 included 1 species that had an aquatic life history or blood feeding
 behavior. Species in Table 3 are species based on the phylogeny from
 Wiegmann et al. 2011.
DOI: 10.5061/dryad.c866t1g6z
title: Sebastes genomic islands of divergence

description: Depth separation is a proposed driver of speciation in marine fishes, with
 marine rockfish (genus Sebastes) providing a potentially
 informative study system. Sebastes rockfishes are
 commercially and ecologically important. This genus encompasses more than
 one hundred species and the ecological and morphological variance between
 these species provides opportunity for identifying speciation-driving
 adaptations, particularly along a depth gradient. A reduced-representation
 sequencing method (ddRADseq) was used to compare 95 individuals
 encompassing six Sebastes species. In this study, we
 sought to identify regions of divergence between species that were
 indicative of divergent adaptation and reproductive barriers leading to
 speciation. A pairwise comparison of S.
 chrysomelas (black-and-yellow rockfish) and S.
 carnatus (gopher rockfish) FST values revealed
 three major regions of elevated genomic divergence, two of which were also
 present in the S. miniatus (vermilion rockfish)
 and S. crocotulus (sunset rockfish) comparison. Thses
 corresponded with regions of both elevated DXY values
 and reduced nucleotide diversity in two cases, suggesting a
 speciation-with-gene-flow evolutionary model followed by post-speciation
 selective sweeps within each species. Limited whole genome re-sequencing
 was also performed to identify mutations with predicted effects
 between S. chrysomelas and S. carnatus. Within
 these islands, we identified important SNPs in genes involved in immune
 function and vision. This supports the concept of depth-driven speciation,
 as these are adaptive vectors noted in other organisms. Additionally,
 changes to genes involved in pigment expression and mate recognition shed
 light on how S. chrysomelas and S.
 carnatus may have become reproductively isolated. 
description: This dataset consists of the STACKS (Catchen et al., 2013)
 outputs from 95 <em>Sebastes</em> samples sequenced using
 double-digest restriction site-associated DNA sequencing (ddRAD-seq,
 Peterson et al. 2012) and then 2x100bp paired-end Illumina sequencing. The
 distribution across the six species was <em>S.
 carnatus </em>(n=20), <em>S.
 chrysomelas </em>(n=20), <em>S.
 miniatus </em>(n=15), <em>S.
 crocotulus </em>(n=16), <em>S. mentella </em>(n=8),
 and <em>S. alutus</em> (n=16). These were aligned against the
 <em>S. schlegelii </em>genome (He et al., 2019) using Bowtie2
 and then processed using the Stacks v2.52 ref_map.pl pipeline. Additional
 flags used for the populations sub-program of STACKS were -p 2 -r 0.50
 --min-maf 0.05 --max-obs-het 0.7 --fstats --smooth-fstats --hwe
 --bootstrap --bootstrap-reps 1000 --vcf --genepop.
 Pairwise <em>F</em><sub>ST</sub> and phistats
 output files were filtered using a blacklist method for Hardy-Weinberg
 disequilibrium in R using the results the GENEPOP v4.4.3 probability test
 (p &lt; 0.001) as well as pool bias, which assessed for genotypic
 association in sequencing library pools using GENEPOP.
DOI: 10.5061/dryad.sqv9s4n43
title: Exposure to a fungal pathogen increases the critical thermal minimum of two frog species Datasets

description: This dataset contains data from a laboratory experiment described in the
 paper: Siddons, S. R., and Searle, C. L. (Accepted). Exposure to
 a fungal pathogen increases the critical thermal minimum of two frog
 species. Ecology and Evolution. The experiment examined how
 exposure to a virulent fungal pathogen, Batrachochytrium dendrobatidis
 (Bd), affected the critical thermal minimum (CTmin) of two frog species,
 Hyla versicolor (gray treefrog) and Lithobates palustris (pickerel frog).
 The CTmin is the minimum thermal performance point of an organism, which
 we estimated via righting response trials. For both frog
 species, the frogs were held in a beaker partially submerged in a
 circulating water at 15°C. At each 1-degree temperature decrease every 2.5
 minutes, the frog was gently flipped onto their back and observed
   for how quickly they were able to right themselves
 ("Decreasing" trial). Frogs were considered unable to right
 themselves when they did not do so within 10 seconds. Another trial was
 conducted for each frog ("Constant" trial ), in which
 they were flipped onto their backs every 2.5 minutes while
 keeping the temperature at a constant 15°C. Main results of the experiment
 are that, for both species, the CTmin was higher for Bd-exposed frogs than
 unexposed frogs, and the CTmin of H. versicolor was higher than L.
 palustris. We also found that Bd-exposed frogs of both species righted
 themselves significantly fewer times in both decreasing and constant
 temperature trials. Finally, we observed higher mortality in Bd-exposed
 individuals throughout the experiment after Bd exposure for both species
 compared to unexposed individuals, with no difference between species.
description: These data were collected by conducting lab-based cold tolerance
 challenges via righting-response tests at Purdue University Life Science
 Animal Building. The data were processed using a series of generalized
 linear mixed models in RStudio to develop a manuscript accepted for
 publication in Ecology and Evolution.
description: The readme files contains a explanation of the variables in the
 dataset, and any measurement units necessary. Information on how the
 measurements were conducted can be found in the manuscript referenced
 above.