cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nk98sf7s0
title: Olive ridley blood volume by nesting strategy

description: Sea turtles dive with a full lung of air and these O2 stores are
 supplemented by O2 stored in blood and muscle.  Olive ridley sea
 turtles exhibit polymorphic nesting behavior; mass nesting behavior called
 arribada, where up to 25,000 turtles will nest at once, and solitary
 nesting behavior. The potential physiological differences between the
 individuals using these strategies are not well understood. We measured
 blood volume and associated variables, including blood hemoglobin content
 and hematocrit, to estimate total blood O2 stores. There were no
 significant differences in mean values between nesting strategies, but
 arribada nesting individuals were more variable than those performing
 solitary nesting. Mass specific plasma volume was relatively invariant
 among individuals but mass specific blood volume and blood oxygen stores
 varied widely, 2-fold and 3-fold, respectively.  Blood O2 stores
 represented 32% of total body O2 stores. Under typical mean diving
 conditions of 26°C and high levels of activity, blood stores confer ~14
 min to aerobic dive times and are likely critical for the long duration,
 deep diving exhibited by the species. Individual differences in blood O2
 stores strongly impact estimated aerobic dive limits and may constrain the
 ability of individuals to respond to changes on ocean climate.
description: Blood volume was measured from evan's blue dilution and
 hematologies in solitary and arribada nesting olive ridley sea turtles.
 Corticosterone, glucose and lactate were measured in the associated
 samples. 
description: S= solitary, A = arribada, BV = blood volume, Hb = hemoglobin,
 Cort= corticosterone
DOI: 10.5061/dryad.vdncjsxs9
title: Data: Using environmental DNA and occupancy modeling to estimate rangewide metapopulation dynamics

description: We demonstrate the power of combining two emergent tools for resolving
 rangewide metapopulation dynamics. First, we employed environmental DNA
 (eDNA) surveys to efficiently generate multi-season rangewide site
 occupancy histories.  Second, we developed a novel dynamic,
 spatial multiscale occupancy model to estimate metapopulation
 dynamics.  The model incorporates spatial relationships,
 explicitly accounts for non-detection bias and allows direct evaluation of
 the drivers of extinction and colonization. We applied these tools to
 examine metapopulation dynamics of endangered tidewater goby, a species
 endemic to California estuarine habitats. We analyzed rangewide eDNA data
 from 190 geographically isolated sites (813 total water samples) surveyed
 from two years (2016 and 2017). Rangewide estimates of the proportion of
 sites that were occupied varied little between 2016 (0.52) and 2017
 (0.51). However, there was evidence of extinction and colonization
 dynamics. The probability of extinction of an occupied site (0.106) and
 probability of colonization of an unoccupied site (0.085) were nearly
 equal. Stability in site occupancy proportions combined with nearly equal
 rates of extinction and colonization suggests a dynamic equilibrium
 between the two years surveyed. Assessment of covariate effects revealed
 that colonization probability increased as the number of occupied
 neighboring sites increased and as distance between occupied sites
 decreased. We show that eDNA surveys can rapidly provide a snapshot of a
 species distribution over a broad geographic range, and when these surveys
 are paired with occupancy modeling, can uncover metapopulation dynamics
 and their drivers.
description: We analyzed rangewide eDNA data from 190 geographically isolated
 sites (813 total water samples) surveyed from two years (2016 and 2017)
 using a spatial, dynamic occupancy model.    
description: Site occupancy, covariate data, neighborhood structure, and data
 file definitions are provided in the files:
 DataDictionary.pdf
 TWGeDNA_2016_2017.csv
 Neighborhood_MatrixV6.3.csv  
 The R code for implementation of the novel dynamic, spatial
 multiscale occupancy model is provided in:
 AnalysisOfGobyData.R
 DynamicOccModel.mcmcFuncs.R
 DynamicOccModelFuncs.cc dMvnCpp.cc
 To run place all files (e.g., data files and R code) in your
 working directory and open and execute "AnalysisOfGobyData.R" in
 R.
DOI: 10.5061/dryad.np5hqbzr4
title: Lateglacial and Holocene pollen and charcoal records for truwana/Cape Barren Island, Bass Strait, southeast Australia.

description: We reconstruct long-term vegetation development in a temperate Australian
 oceanic setting using wetland sediments, pollen and charcoal records from
 truwana/Cape Barren Island in Bass Strait to reconstruct vegetation and
 fire history. Magnetic susceptibility and organic content were also
 derived for two of the four sites considered as proxies for local
 sedimentary changes. Result shows that the lateglacial landscape
 (14,000–13000 cal yr BP) was characterized by open grassy Eucalyptus
 woodland in Bass Strait, and Eucalyptus woodland cover increased during
 the early Holocene (13,000–9000 cal yr BP), with high fire activity. Scrub
 and heathland generally dominated by Leptospermum, Melaleuca,
 Allocasuarina/Casuarina and Ericaceae taxa expanded in the last 9000 years
 at the expense of Eucalyptus woodland, with a major decline in fire
 activity after 5000 cal yr BP until the last 200 years. Woodland elements
 (Eucalyptus, Callitris) increased slightly at some sites in the last 2000
 years.
description: For pollen analysis,
 samples were taken from sediment cores at 1–4-cm intervals and samples
 were processed following standard pollen preparation procedures, which
 included HCl, KOH and acetolysis treatments. At least 300 terrestrial
 pollen grains were identified on slides except for a few depths with
 extremely low pollen concentrations in which 100 to 150 pollen grains were
 counted. Pollen and spores were identified using the Australasian Pollen
 and Spore Atlas (http://apsa.anu.edu.au/) and PalaeoWorks reference collections at the Australian National University’s Archaeology and Natural History Laboratory. Microscopic charcoal particles (&lt;125 µm) were also counted on pollen slides. For macrocharcoal ( &gt;125 and &gt;250 µm) analysis, contiguous sediment samples were taken from cores and analysed, following the method of Whitlock & Larsen (2001). Big Reedy Lagoon and truwana East Coast Lagoon cores were scanned for trace metals and magnetic susceptibility using ITRAX at the Australian Nuclear Science and Technology Organisation. The ratio for molybdenum incoherence/coherence (Mo inc/Mo coh) was used as a proxy for organic content. Chronology (aga-depth model) is based on Accelerator Mass Spectrometry (AMS) <sup>14</sup>C dates (Bacon, SHCal13). For YL and tECL age-depth models, <i>Pinus</i> pollen is used as an age marker for approximately 150 yr BP. Sediment core locations: Big Reedy Lagoon (40.3589°S, 148.2381°E, 26 m asl), Yakka Lagoon (40.3589°S, 148.2447°E, 30 m asl), truwana East Coast Lagoon (40.3311°S, 148.2381°E, 1m asl) and Green Lagoon (40.442967°S, 148.143840°E, 10 m asl). Reference Whitlock, C., & Larsen, C. (2001). Charcoal as fire proxy. In J. P., Smol, et al. (Eds.), <i>Tracking environmental change using lake sediments: terrestrial, algal, and siliceous indicators, </i>3. Kluwer Academic Publishers, Dordrecht, The Netherlands.
DOI: 10.5061/dryad.0gb5mkkzz
title: Data from: Plasticity via feedback reduces the cost of developmental instability

description: Costs of plasticity are thought to have important physiological and
 evolutionary consequences. A commonly predicted cost to plasticity is that
 plastic genotypes are likely to suffer from developmental instability.
 Adaptive plasticity requires that the developing organism can in some way
 sense what environment it is in or how well it is performing in that
 environment. These two information pathways—an “environmental signal” or a
 “performance signal” that indicates how well a developing phenotype
 matches the optimum in the current environment—can differ in their
 consequences for the organism and its evolution. Here, we consider how
 developmental instability might emerge as a side-effect of these two
 distinct mechanisms. Because a performance cue allows a regulatory
 feedback loop connecting a trait to a feedback signal, we hypothesized
 that plastic genotypes using a performance signal would be more
 developmentally robust compared to those using a purely environmental
 signal. Using a numerical model of a network of gene interactions, we show
 that plasticity comes at a cost of developmental instability when the
 plastic response is mediated via an environmental signal, but not when it
 is mediated via a performance signal. We also show that a performance
 signal mechanism can evolve even in a constant environment, leading to
 genotypes pre-adapted for plasticity to novel environments even in
 populations without a history of environmental heterogeneity.
description: Data collected through numerical simulations.
description: Here are explanations of the meaning of each column in the
 dataset: meanP: Mean phenotypic value over all
 replicated development of the genotype of interest.
 sdP: Standard deviation in phenotypic value among all replicated
 development of the genotype of interest. meanW: Mean
 fitness over all replicated development of the genotype of
 interest. sdW: Standard deviation in fitness among all
 replicated development of the genotype of interest.
 trait_optima: Optimal trait in the environment
 considered. nbGenes: Number of genes.
 Project: A coded name of the set of simulation. It is kept here
 in the daat for backward verification. Each project correspond to a unique
 treatment. Replicate: Simulation index in the
 project. Generation: Generation sampled.
 Environment: Type of environment. Signal: Type
 of signal.
DOI: 10.15468/dl.jxdjwg
title: Occurrence Download

description: A dataset containing 236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Livistona saribus"
 ]
}

 The dataset includes 236 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002614-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ttdz08kwg
title: Impact of landscape fragmentation and climate change on body size variation of bumblebees during the last century

description: Body size is a key parameter of organism fitness. While the impact of
 climate change on body size has received increasing attention, the
 long-term consequences of landscape fragmentation are still poorly known.
 These two major global threats may potentially induce opposite trends: the
 decrease of body size in warmer environments (e.g. individuals developing
 faster) or the selection of larger individuals in fragmented habitats
 (e.g. large individuals more capable of reaching distant patches). We
 assessed the relationship between temperature and landscape fragmentation
 with mean body size during the last century, within four European regions
 (Austria, Belgium, England and above the Arctic circle in Scandinavia) and
 among queens of five bumblebee species. At the regional scale, we first
 analysed the variation over time of body size and the two hypothesised
 drivers, temperature and landscape fragmentation. Then, at the local
 landscape scale, we tested whether body size varied according to these
 drivers irrespective of the region. At the regional level, we observed a
 statistically clear increase of queen body size corresponding to an
 increase of landscape fragmentation (i.e. in Belgium and England). There
 was no increase of size when fragmentation did not increase (i.e. in
 Austria and above the Arctic Circle). Temperature also increased through
 time in all regions. At the local landscape scale, we found that all
 species were impacted by changes in both climate and landscape
 fragmentation but show different trends. The body size of the two largest
 species significantly increased at landscape level with higher
 fragmentation while body size of the two smallest species decreased with
 higher fragmentation. We highlight that, in a context of global changes,
 landscape fragmentation can also be a major driver of body size clines.
 Depending on the dispersal abilities of species, larger species could be
 positively selected for and overcome landscape fragmentation.
DOI: 10.5061/dryad.dbrv15f06
title: Rainfall continentality, via the winter GAMS angle, provides a new dimension to biogeographical distributions in the Western United States

description: Aim: Drought stress, and its effects on the biogeography of vegetation,
 has focused primarily on water availability during the growing season,
 thus focusing primarly on summer. However, variation in rainfall
 continentality (i.e., the continental interior being insulated from
 oceanic influences) can produce striking vegetation differences. We aim to
 disentangle summer water balance from the influence of rainfall
 continentality on winter rainfall, to better understand how climate
 regulated the distributions of woody plants in the Western USA. Location:
 Western USA. Time period: Actual. Major taxa studied: Angiosperms and
 Conifers. Method: We used Redundancy Analysis (RDA) to investigate
 correlations between rainfall continentality, summer water balance,
 minimum winter temperature and length of growing season on the
 distributions of 130 tree and shrub species in 467 plots. Rainfall
 continentality was calculated using the Gams (1932) index, modified for
 winter precipitation, and summer water balance with the ratio of summer
 precipitation to temperature. We estimated Actual EvapoTranspiration
 (AET), Deficit (DEF), mean annual temperature and rainfall from global
 gridded datasets and correlated them with RDA axes. Results: Rainfall
 continentality measured with the Gams index and minimum temperatures best
 explained the contrast between oceanic vegetation in the Pacific Coast
 Ranges and continental vegetation in the Intermountain Region and Rocky
 Mountains. Growing Season Length (GSL) was the second strongest factor
 correlated with vegetation distributions. Summer water balance, despite
 being the most widely used climatic factor to assess drought stress in
 biogeography, was the third strongest factor correlating with vegetation
 classes of the western US. AET was equally correlated with RDA axes 1 and
 3, and, thus, could not discriminate between the contrasts in the RDA.
 Main conclusions: Rainfall continentality measured with the winter Gams
 index provides a more precise metric than summer water balance for
 understanding how the biogeography of woody plants in the western USA is
 regulated by climate. Broadly integrating the Gams index of continentality
 into plant distributions may improve our understanding of biogeographical
 distributions, the evolution of subspecies in species that span coastal to
 interior regions, and predictions of responses to climate change.
DOI: 10.5061/dryad.76hdr7sv3
title: On the potential of Angiosperms353 for population genomics studies

description: Premise of the Study: Targeted sequencing using Angiosperms353 has emerged
 as a low-cost tool for phylogenetics, with early results spanning from all
 flowering plants to within genera. The use of universal markers at
 narrower scales—within populations— would eliminate the need for specific
 marker development while retaining the benefits of full-gene sequences.
 However, whether the Angiosperms353 markers provide sufficient variation
 within species to calculate demographic parameters is untested. Methods:
 Using herbarium specimens from a 50-year-old floristic survey of Guadalupe
 Mountains National Park, we sequenced 95 samples from 24 species using
 Angiosperms353. We adapted a data workflow to process targeted sequencing
 data that calls variants within each species and prepares data for
 population genetic analysis. We calculated genetic diversity using
 standard metrics (e.g. heterozygosity, pi). Key Results: Angiosperms353
 gene recovery was associated with genomic library concentration, with
 limited phylogenetic bias. We identified over 1000 segregating variants
 with zero missing data within 22 of 24 species. A subset of these variants
 were filtered to remove linked SNPs, revealing high heterozygosity in many
 species. Pairwise nucleotide diversity (pi) was typically between 0.002
 and 0.010, with much of the variation in noncoding regions flanking the
 targeted sequences. Conclusions: Despite sequencing few individuals per
 species, the Angiosperms353 markers contained sufficient variation to
 calculate demographic parameters. Larger sampling within species will
 allow for estimating gene flow and population dynamics in any angiosperm.
 Our study will benefit conservation genetics, where Angiosperms353
 provides universal repeatable markers, low missing data, and haplotype
 information and the use of herbarium specimens.
description: Target capture sequencing using Angiosperms353. Sequenced
 assembled using HybPiper to identify the longest supercontig sequence per
 species. Reads for each species aligned to these reference sequences using
 bwa and variants called with the GATK Exome Best Practices
 Pipeline.
DOI: 10.15468/dl.d5u623
title: Occurrence Download

description: A dataset containing 10146 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gerrhosauridae"
 ]
}

 The dataset includes 10146 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002612-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8pg8j
title: Tick parasitism impairs contest behavior in the western fence lizard (Sceloporus occidentalis)

description: Parasites may impair host behavior in ways that reduce host fitness,
 especially when access to territories or mates becomes disrupted. Western
 fence lizards (Sceloporus occidentalis) are a key host to western
 black-legged ticks (Ixodes pacificus). Males are highly aggressive during
 the mating season, competing with rivals through displays of color badges,
 pushups, and other behaviors. We hypothesized that experimental tick
 infestation diminishes the performance of male western fence lizards in
 intrasexual contests, via either blood loss, damage to sensory structures
 or both. We infested males with larval ticks and staged contests between
 infested and quality-matched control males, and measured their behavior in
 enclosure arenas. Infested lizards were less aggressive and exhibited
 decreased hematocrit, compared to non-infested animals. We found no
 relationships between aggression and either body size or blue ventral
 badge color traits. There was also no effect of tick attachment location
 and hemoparasite infection on host contest behavior. This is the first
 demonstration of the impact of I. pacificus parasitism on intraspecific
 interactions of western fence lizards, and suggests that tick infestation
 has substantial impacts on lizard fitness. Because I. pacificus rely
 heavily on these lizards for blood meals and dispersal, these impacts
 could also influence the abundance of ticks and the pathogens they vector.
  
description: Behavior data collected using BORIS with video playbacks of
 encounters between male Sceloporus occidentalis in enclosures. Data
 processed in R 4.0.0. 
description: See README.txt in upload.
DOI: 10.5061/dryad.z612jm69m
title: Developmental and water deficit-induced changes in hydraulic properties and xylem anatomy of tomato fruit and pedicel

description: Xylem water transport from the parent plant into the fruit plays a crucial
 role in fruit growth, development, and quality formation. Current research
 on fruit hydraulics has attempted to partition the hydraulic resistance of
 the pathway over development. However, no consensus has been reached and
 this question has not been addressed in the context of changing plant and
 fruit water status under water deficit. We rigorously investigated the
 developmental changes of hydraulic property of the fruit and pedicel under
 well-irrigated condition and water deficit based on hydraulic
 measurements, fruit rehydration, dye tracing, light and electron
 microscopy, and flow modeling. A decline in water transport capacity did
 not occur in the pathway prior to the fruit, but within the fruit itself,
 which might lie in the xylem and/or outside-xylem pathway. The
 developmental pattern of pathway hydraulic resistance was not
 significantly influenced by water deficit. The changed xylemic water flow
 between the fruit and the parent plant due to a reduced driving force
 under water deficit could explain the reduced fruit water accumulation.
 This work provides new insights into the understanding of xylem water
 transport in fleshy fruits and its sensitivity to water deficit from a
 hydraulics perspective.
DOI: 10.5061/dryad.2547d7wpb
title: Evaluating spatially explicit sharing-sparing scenarios for multiple environmental outcomes

description: 1. Understanding how to allocate land for the sustainable delivery of
 multiple, competing objectives is a major societal challenge. The land
 sharing-sparing framework presents a heuristic for understanding the
 trade-off between food production and biodiversity conservation by
 comparing region-wide land use scenarios which are equivalent in terms of
 overall food production. 2. Here, for two contrasting regions of lowland
 England (The Fens and Salisbury Plain), we use empirical data and
 predictive models to compare a suite of spatially explicit scenarios
 reflecting the full range of the sharing-sparing continuum, including
 mixed scenarios which combine elements of both sharing and sparing. We
 evaluate a range of outcomes (bird populations, global warming potential
 (GWP), nitrogen and phosphorus pollution and outdoor recreation), in order
 to identify approaches to regional land use planning with the potential to
 deliver multiple societal benefits. 3. Land-sharing scenarios (which
 reduce the dominance of productive agricultural land in farmed areas and
 the area of larger unfarmed areas) result in negative outcomes,
 particularly for birds and GWP. In contrast, many land-sparing scenarios
 (including mixed scenarios which increase the area of lower-yield farmland
 alongside larger unfarmed areas) resulted in improvements in all or most
 outcomes, although for recreation and nutrient export differences between
 scenarios were modest. 4. Importantly, environmental outcomes also
 depended on the spatial arrangement of spared land, the types of natural
 or semi-natural habitat promoted on spared land, whether some lower-yield
 farmland is delivered alongside larger unfarmed areas, and the overall
 region-wide food production target. 5. Policy implications. Our study
 suggests that land-sparing strategies which increase the area of natural
 and seminatural areas can improve environmental outcomes, despite the
 costs associated with high-yield agriculture. However, high-yield
 agriculture should not compromise future production or ecosystem services
 on spared land, and explicit policies such as certification or payments
 for ecosystem services are required to link sustainable high-yield
 production to habitat conservation. Our study also highlights the
 importance of mitigating projected increases in food demand.
description: Modelled properties of each land use scenario. See associated
 manuscript for full description. 
description: See ReadMe.txt for description of variables