cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f1vhhmgtv
title: Data from: Phytoplankton growth and stoichiometric responses to warming, nutrient addition and grazing depend on lake productivity and cell size

description: Global change involves shifts in multiple environmental factors that act
 in concert to shape ecological systems in ways that depend on local biotic
 and abiotic conditions. Little is known about the effects of combined
 global change stressors on phytoplankton communities, and particularly how
 these are mediated by distinct community properties such as productivity,
 grazing pressure and size distribution. Here, we tested for the effects of
 warming and eutrophication on phytoplankton net growth rate and C:N:P
 stoichiometry in two phytoplankton cell size fractions (&lt;30 μm and
 &gt;30 μm) in the presence and absence of grazing in microcosm
 experiments. Because effects may also depend on lake productivity, we used
 phytoplankton communities from three Dutch lakes spanning a trophic
 gradient. We measured the response of each community to multifactorial
 combinations of temperature, nutrient, and grazing treatments and found
 that nutrients elevated net growth rates and reduced carbon:nutrient
 ratios of all three phytoplankton communities. Warming effects on growth
 and stoichiometry depended on nutrient supply and lake productivity, with
 enhanced growth in the most productive community dominated by
 cyanobacteria, and strongest stoichiometric responses in the most
 oligotrophic community at ambient nutrient levels. Grazing effects were
 also most evident in the most oligotrophic community, with reduced net
 growth rates and phytoplankton C:P stoichiometry that suggests
 consumer‐driven nutrient recycling. Our experiments indicate that
 stoichiometric responses to warming and interactions with nutrient
 addition and grazing are not universal but depend on lake productivity and
 cell size distribution.
description: This multifactorial
 microcosm experiment tested for the effects of warming and eutrophication
 on phytoplankton net growth rate and C:N:P stoichiometry in two
 phytoplankton cell size fractions (&lt;30 μm and &gt;30 μm), in
 the presence and absence of grazing. We measured the response of
 phytoplankton communities (collected from 3 lakes spanning a trophic
 gradient), to multifactorial combinations of ambient and elevated
 temperature, nutrient, and grazing treatments, over a 6-day
 period.
description: Empty cells indicate missing values. Explanation of parameters is
 provided in the tab 'metadata'.
DOI: 10.5061/dryad.2rbnzs7kn
title: Data from: Biological stoichiometry of oleaginous microalgal lipid synthesis: The role of N:P supply ratios and growth rate on microalgal elemental and biochemical composition

description: Biological Stoichiometry is an ecological framework connecting the balance
 of elements to the functioning of organisms. Here, we applied this
 framework to study the relationships between carbon:nitrogen:phosphorus
 (C:N:P) ratios and synthesis of industrial high value biochemicals in the
 highly oleaginous alga Tetradesmus bernardii. We expected an increase in
 protein content with increasing cellular N content and decreasing C:N
 stoichiometry, and an increase in lipid content with increasing C:N and
 C:P stoichiometry. We tested these hypotheses by exposing T. bernardii to
 N and P limitation at a range of N:P supply ratios in chemostats set at
 low and high dilution rates. Following expectations, the cellular protein
 content increased with the N content, and decreased with cellular C:N
 ratios across all treatments. Carbohydrates and lipids largely followed
 the relative availability of C and increased under both N and P
 limitation, with higher C:N and C:P ratios. Specifically, lipid content
 increased by 100–125% upon N and P limitation, with a shift towards more
 neutral lipids at the cost of glycolipids and phospholipids. Generally, we
 observed a re-allocation of cellular C from protein to carbohydrates upon
 modest N limitation, and towards lipids under P and severe N limitation.
 Our results demonstrate stoichiometrically predictable patterns of
 industrially valuable compounds in an oleaginous microalga.
description: This data was derived from
 a series of flat panel chemostat experiments with the
 microalga <em>Tetradesmus bernardii</em> exposed to a range of
 N:P supply (N:P=1.5, 4.4, 17, and 522) ratios under low (0.2) and high
 (0.6) dilution rates. Experiments were performed with three
 replicates. 
description: This dataset provides data from each replicated treatment.
DOI: 10.5061/dryad.h44j0zph7
title: Sex-specific transgenerational plasticity II: Grandpaternal effects are lineage- and sex-specific in threespined sticklebacks

description: 1. Transgenerational plasticity (TGP) occurs when the environment
 encountered by one generation (F0) alters the phenotypes of one or more
 future generations (e.g. F1 and F2). Sex selective TGP, via specific
 lineages or to only male or female descendants, has been underexplored in
 natural systems, and may be adaptive if it allows past generations to
 fine-tune the phenotypes of future generations in response to sex-specific
 life history strategies.  2. We sought to understand if exposing
 males to predation risk can influence grandoffspring via sperm in
 threespined stickleback (Gasterosteus aculeatus). We specifically tested
 the hypothesis that grandparental effects are transmitted in a
 sex-specific way down the male lineage, from paternal grandfathers to F2
 males.   3. We reared F1 offspring of unexposed and
 predator-exposed F0 males under ‘control’ conditions and used them to
 generate F2s with control grandfathers, a predator-exposed maternal
 grandfather (i.e., predator-exposed F0 males to F1 daughters to F2
 offspring), a predator-exposed paternal grandfather (i.e.,
 predator-exposed F0 males to F1 sons to F2 offspring), or two
 predator-exposed grandfathers. We then assayed male and female F2s for a
 variety of traits related to antipredator defense.  4. We found
 little evidence that transgenerational effects were mediated to only male
 descendants via the paternal lineage. Instead, grandpaternal effects
 depended on lineage and were mediated largely across sexes, from F1 males
 to F2 females and from F1 females to F2 males. When their paternal
 grandfather was exposed to predation risk, female F2s were heavier and
 showed a reduced change in behavior in response to a simulated predator
 attack relative to offspring of control, unexposed grandparents. In
 contrast, male F2s showed reduced antipredator behavior when their
 maternal grandfather was exposed to predation risk. However, these
 patterns were only evident when one grandfather, but not both
 grandfathers, was exposed to predation risk, suggesting the potential for
 non-additive interactions across lineages. 5. If sex-specific and lineage
 effects are common, then grandparental effects are likely underestimated
 in the literature. These results draw attention to the importance of
 sex-selective inheritance of environmental effects and raise new questions
 about the proximate and ultimate causes of selective transmission across
 generations.
description: All behavioral and
 morphological data were collected live on paper and transcribed
 electronically. Cortisol data were calculated from OD scores.
DOI: 10.5061/dryad.x69p8czg6
title: Wild at heart: programs to diminish negative ecological and evolutionary effects of conservation hatcheries

description: Hatchery programs are critical for conservation and management of many
 imperiled fishes. Most traditional aquaculture programs negatively affect
 ecological performance, genetic, and phenotypic diversity of
 hatchery-origin fish compared with wild counterparts. Here, we synthesize
 outcomes of three conservation programs aimed at enhancing ‘wildness’.
 Each program focuses on a different species: lake sturgeon, razorback
 sucker, and Rio Grande silvery minnow. These species differ in key life
 history traits including size and age at sexual maturity, reproductive and
 migratory behavior, and habitat requirements. Threats to persistence of
 the focal taxa, however, exemplify common pressures experienced by
 freshwater fishes worldwide. Conservation hatchery programs for lake
 sturgeon, razorback sucker, and Rio Grande silvery minnow capitalize on
 natural spawning in the wild followed by collections of wild-fertilized
 eggs/larvae for hatchery rearing. Individuals are repatriated to the wild
 after rearing to body sizes less susceptible to mortality. Protocols
 include collections of eggs or larvae across the entire spawning period
 and at appropriate geographic scales to maximize retention of genetic
 diversity and, to increase the likelihood of preserving variation for
 heritable life history traits. Using direct and indirect evidence we show
 that hatchery programs that allow individuals to fulfill parts of the
 life-cycle in their native habitats can be conducted without compromising
 genetic diversity. Adoption of similar strategies in other imperiled
 fishes would improve understanding of species life history, and provide an
 incentive to protect native habitats so they may eventually support
 self-sustaining populations.
description: Mitochondrial DNA data for Rio Grande silvery minnow was collcted
 using Sanger sequencing and Single Standed Conformational Polymorphism
 (SSCP) Microsatellite data for Rio Grande silvery
 minnow was collected by PCR and electrophoresis on a ABI3130
 sequencher. Microsatellite sizes were determined using
 ABI Genemapper software. All genotypes were verified by visual inspection
 of the chromatogram. Mitochondrial DNA data for
 Razorback sucker was collected using using Sanger sequencing.
 Microsatellite data for Razorback sucker was collected by PCR and
 electrophoresis on a LI-COR sequencher.
DOI: 10.5061/dryad.1rn8pk0rb
title: Data for: Comparing the effect of landscape context on vascular plant and bryophyte communities in a human-dominated landscape

description: Aims: It is important to understand the effect of landscape context on
 biological communities to predict how biodiversity will be affected on
 human-dominated landscapes. While many studies have tested the effects of
 landscape context on the species richness and composition of vascular
 plants, few have compared the responses of vascular plants and bryophytes
 on the same landscape. We sampled non-epiphytic bryophytes and vascular
 plants in 184 plots to test whether three landscape context factors
 measured four years or four decades previously could predict bryophyte or
 vascular plant species richness and composition after accounting for local
 factors. Location: Temperate forests and oak savannahs, Vancouver
 Island, British Columbia, Canada. Methods: We used model selection and
 comparisons to test the effects of surrounding road density, total amount
 of forest, and distance to the nearest forest edge on species richness,
 species richness of non-disturbance-associated species, and community
 composition after controlling for important local predictors including
 substrate availability and topography. Results: The species richness of
 non-disturbance-associated vascular plants was lower in plots with greater
 surrounding historical road density, and perennial stayer bryophyte
 richness declined with increasing historical road density and lower
 historical forest amount, suggesting a potential extinction debt.
 Landscape context significantly affected total species richness and
 community composition of vascular plants, but not bryophytes. Conclusion:
 While bryophytes appear to be less sensitive overall to landscape context
 than vascular plants, disturbance-intolerant perennial stayer bryophytes
 may decline in the future in response to the increased road density and
 loss of forest cover that has occurred over the past four decades.
description: We sampled 184 20m x 20m
 relevé plots on the Saanich Peninsula, a region of approximately 330
 km<sup>2 </sup>in 2009. In each plot, we identified all
 vascular plants and estimated the percent cover of each. We also
 identified all bryophyte species occurring on soil, rock, or decomposing
 wood, and estimated the percent cover of each. If a species was estimated
 to cover less than 1% of the plot, we entered “0.5” in the data, and if it
 covered much less than 1%, we entered “0.1”. We did not survey epiphytic
 bryophytes on living trees. We also measured the slope and aspect of each plot,
 and estimated the percent cover of soil, exposed rock, and decomposing
 wood substrate. We then used a Geographical Information System (GIS) to
 measure the total amount of natural vegetated area within a 500m buffer of
 each plot, the total length of roads within the same distance of each
 plot, and the distance in metres from the plot to the nearest edge between
 natural and non-natural vegetation.
DOI: 10.5061/dryad.18931zctw
title: Microsatellite genotype data from seven loci for a phylogeographic/population genetic study of the South African endemic freshwater crab Potamonautes lividus sampled from eight localities in the KwaZulu-Natal and Eastern Cape provinces in South Africa

description: During the present study, the phylogeography of the only southern African
 IUCN Red Listed vulnerable (VU) freshwater crab, Potamonautes
 lividus was investigated by surveying several localities
 in the Eastern Cape and KwaZulu-Natal provinces in South
 Africa. Both nuclear and mitochondrial DNA markers were used, and
 it was hypothesized, that marked genetic differentiation should be
 present, while niche modeling was undertaken to explore the distribution
 of the species along the east coast of South Africa. Further, the
 shortfalls in the present approach to IUCN Red Listing, as illustrated by
 a vulnerable species of crabs are discussed. Results from the mtDNA
 revealed the presence of two haploclades confined to specimens from the
 two provinces respectively and the general absence of maternal dispersal;
 a fact that was further validated by the marked FST data
 and high FST. Within the Eastern Cape haploclade, low
 frequency maternal dispersal occurred, corroborated by
 the low FST. In contrast, no
 haplotypes were shared in the KwaZulu-Natal haploclade a fact corroborated
 by marked FST differences.  The microsatellite
 data demonstrated the presence of higher frequency, possibly paternally
 biased dispersal of specimens between the Eastern Cape and KwaZulu-Natal
 provinces. Our results suggest that presence of two distinct
 management units within P. lividus. Divergence time
 estimation suggest a late Pleistocene cladogenesis between the Eastern
 Cape and KwaZulu-Natal haploclades.  Considering the presence
 of P. lividus in several newly collected nature
 conservation areas in both provinces, and its potential presence in the
 intermediary area based on the MAXENT niche modeling, our data
 suggest the species IUCN Red Listing status should be downgraded to LC. A
 comparison of all the EN, VU and CR IUCN Red Listed freshwater crabs for
 the entire Afrotropical region reveals the lack of recent sampling in the
 three biodiversity hotspots in West, Central and East Africa, with
 mountainous areas containing a disproportionate number of species with
 most species being devoid of phylogeographic study. 
description: Microsattelite data
description: The data are presented as an Excel spreadsheet in GenAlEx
 format
DOI: 10.15468/dl.bvxvdt
title: Occurrence Download

description: A dataset containing 35572 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Cecropia peltata, Cecropia palmata, Cecropia pachystachya)"
 ]
}

 The dataset includes 35572 records from 616 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002459-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v41ns1rt2
title: Data from: Epigenetic potential and DNA methylation in an ongoing House Sparrow (Passer domesticus) range expansion

description: During range expansions, organisms can use epigenetic mechanisms to adjust
 to conditions in novel areas by altering gene expression and enabling
 phenotypic plasticity. Here, we predicted that the number of CpG sites
 within the genome, one form of epigenetic potential, would be important
 for successful range expansions because DNA methylation can modulate gene
 expression, and consequently plasticity. We asked how the number of CpG
 sites and DNA methylation varied across five locations in the ~70 year-old
 Kenyan house sparrow ( Passer domesticus ) range expansion. We found that
 the number of CpG sites was highest towards the vanguard of the invasion
 and decreased towards the range core. Analysis suggests that this pattern
 may have been driven by selection, favoring birds with more CpG sites at
 the range edge. However, we cannot rule out other processes including
 non-random gene flow. Additionally, DNA methylation did not change across
 the range expansion, nor was it more variable. We hypothesize that as new
 areas are colonized, epigenetic potential may be selectively advantageous
 early but eventually be replaced by less plastic and perhaps
 genetically-canalized traits as populations adapt to local conditions.
 While further work is needed on epigenetic potential, this form (CpG
 number) appears to be a promising mechanism to investigate as a driver of
 expansions via capacitated phenotypic plasticity in other natural and
 anthropogenic range expansions.
DOI: 10.5061/dryad.41ns1rnbp
title: Supplemental tables from: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are dependent on RORγ

description: Previous studies showed that non-calcemic 20(OH)D3, a product of CYP11A1
 action on vitamin D3, has antifibrotic activity in human dermal
 fibroblasts and in a bleomycin mouse model of scleroderma. In this study
 we tested the role of RORγ, which is expressed in skin, in the action of
 CYP11A1-derived secosteroids using murine fibroblasts isolated from the
 skin of wild type (RORg+/+), knock out (RORg-/-) and heterozygote
 (RORg+/-) mice. CYP11A1-derived 20(OH)D3, 20,23(OH)2D3, 1,20(OH)2D3, and
 1,20,23(OH)3D3 inhibited proliferation of RORγ+/+ fibroblasts in a
 dose-dependent manner with a similar potency to 1,25(OH)2D3. Surprisingly,
 this effect was reversed in RORγ+/- and RORγ-/- fibroblasts with the most
 pronounced stimulatory effect seen in RORγ-/- fibroblasts. All of the
 analogs tested inhibited TGF-β1-induced collagen synthesis in RORγ+/+
 fibroblasts and the expression of other fibrosis-related genes. This
 effect was curtailed or reversed in RORγ-/- fibroblasts. These results
 show that the antiproliferative and antifibrotic activities of the vitamin
 D hydroxy-derivatives are dependent on a functional RORγ. The dramatic
 changes in the transcriptomes of fibroblasts of RORg-/- versus wild type
 mice following treatment with 20(OH)D3 or 1,20(OH)2D3 provide a molecular
 basis to explain, at least in part, the observed phenotypic differences
description: Data were analyzed with Ingenuity Pathway Analysis (Ingenuity®
 Systems, www.ingenuity.com).
 For generating networks, a data set containing gene identifiers and
 corresponding expression values was uploaded into the application. Each
 identifier was mapped to its corresponding object in Ingenuity’s Knowledge
 Base. A fold change cutoff of +/-2 was set to identify molecules whose
 expression was significantly differentially regulated. These molecules,
 called Network Eligible molecules, were overlaid onto a global molecular
 network developed from information contained in Ingenuity’s Knowledge
 Base. Networks of Network Eligible Molecules were then algorithmically
 generated based on their connectivity. The Functional Analysis identified
 the biological functions and/or diseases that were most significant to the
 entire data set. Molecules from the dataset that met the fold change
 cutoff of +/-2 and were associated with biological functions and/or
 diseases in Ingenuity’s Knowledge Base were considered for the analysis.
 Right-tailed Fisher’s exact test was used to calculate the p-value
 determining the probability that each biological function and/or disease
 assigned to that data set is due to chance alone.
DOI: 10.5061/dryad.83bk3j9pb
title: Shared geographic histories and dispersal contribute to congruent phylogenies between amphipods and their microsporidian parasites at regional and global scales

description: In parasites that strongly rely on a host for dispersal, geographic
 barriers that act on the host will simultaneously influence parasite
 distribution as well. If their association persists over macroevolutionary
 time it may result in congruent phylogenetic and phylogeographic patterns
 due to shared geographic histories. Here, we investigated the level of
 congruent evolutionary history at a regional and global scale in a highly
 specialised parasite taxon infecting hosts with limited dispersal
 abilities: the microsporidians Dictyocoela spp. and their amphipod hosts.
 Dictyocoela can be transmitted both vertically and horizontally and is the
 most common microsporidian genus occurring in amphipods in Eurasia.
 However, little is known about its distribution elsewhere. We started by
 conducting molecular screening to detect microsporidian parasites in
 endemic amphipod species in New Zealand; based on phylogenetic analyses,
 we identified nine species-level microsporidian taxa including six
 belonging to Dictyocoela. With a distance-based cophylogenetic analysis at
 the regional scale, we identified overall congruent phylogenies between
 Paracalliope, the most common New Zealand freshwater amphipod taxon, and
 their Dictyocoela parasites. Also, hosts and parasites showed similar
 phylogeographic patterns suggesting shared biogeographic histories.
 Similarly, at a global scale, phylogenies of amphipod hosts and their
 Dictyocoela parasites showed broadly congruent phylogenies. The observed
 patterns may have resulted from covicariance and/or codispersal,
 suggesting that the intimate association between amphipods and Dictyocoela
 may have persisted over macroevolutionary time. We highlight that shared
 biogeographic histories could play a role in the codiversification of
 hosts and parasites at a macroevolutionary scale.
description: Nucleotide sequences used
 in these alignment files were obtained from GenBank or generated by the
 authors. All the sequences used here are available in GenBank. Please see
 Appendix_2 of the manuscript for further information.
DOI: 10.5061/dryad.r4xgxd29d
title: The δ13C series of different components from Masson pine

description: The idea of this study is to analyze the effects of climatic drivers on
 the radial growth (total ring width, earlywood width, and latewood width)
 and the δ13C series of different wood components (whole wood, α-cellulose,
 and holocelluose) from Masson pine in subtropical China. Pairwise
 correlation is significant between three ring width parameters. Earlywood
 and latewood width did not reveal much stronger climatic sensitivity
 rather than total ring width. This indicates that the use of intra-annual
 ring width maybe have little benefit in extracting more climate
 information. The mean δ13C series of the three components of the total
 ring had the strongest climatic response to the July–September relative
 humidity (r= -0.792 (whole wood, WW), -0.758 (holocellulose, HC) and
 -0.769 (α-cellulose, AC)). These results suggest that whole wood from
 Masson pine is sufficient to enhance the climate signal without cellulose
 isolation. Through both stationary temporal and spatial-statistical
 perspectives, the moisture drivers (summer/autumn) had a significant
 impact on three ring width parameters and three components of Masson pine.
 Overall, the tree ring width parameters and the δ13C series from the total
 ring showed a different response to the same climate drivers during the
 same period. The δ13C series may be a more representative climate proxy
 than tree-ring width parameters for the dendroclimatology in subtropical
 China.