cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rb075
title: Data from: Counteracting effects of a non-native prey on demography of a native predator culminate in positive population growth

description: Identifying impacts of non-native species on native populations is central
 to conservation and ecology. While effects of non-native predators on
 native prey populations have recently received much attention, impacts of
 introduced prey on native predator populations are less understood.
 Non-native prey can influence predator behavior and demography through
 direct and indirect pathways, yet quantitative assessments of the relative
 impacts of multiple, potentially counteracting, effects on native predator
 population growth remain scarce. Using ≈20 years of range-wide monitoring
 data, we tested for effects of a recently-introduced, rapidly-spreading
 non-native prey species (Pomacea maculata) on the behavior and demography
 of the endangered snail kite (Rostrhamus sociabilis). Previous studies
 found that food-handling difficulties caused by the large size of P.
 maculata (relative to the native P. paludosa) can lead to energetic
 deficiencies in juvenile kites, suggesting the potential for evolutionary
 traps to occur. However, high densities of P. maculata populations could
 facilitate kites by providing supplemental food resources. Contrary to
 prior hypotheses, we found that juvenile apparent survival increased ≈50%
 in wetlands invaded by non-native snails. Breeding rates and number of
 young fledged/successful nest were also positively associated with
 non-native snail presence, suggesting direct trophic benefits to kites. We
 found no direct effects of the invasive snail on adult survival or daily
 nest survival rates. Kite movements and breeding distribution closely
 tracked the spread of non-native snail populations. Since 2005, kites have
 been heavily concentrated in northern regions where non-native snails have
 established. This geographic shift has had hidden costs, as use of
 northern regions is associated with lower adult survival. Despite negative
 impacts to this key vital rate, matrix population modeling indicated that
 the multifarious effects of the non-native snail invasion on kites
 culminated in increased population growth rates, likely lowering
 short-term extinction risks. Results suggest that considering only
 particular components of behavior or demography may be inadequate to infer
 the population-dynamic importance of non-native prey on native predators,
 including their role in creating potential evolutionary traps. Our
 findings provide information pertinent to Everglades restoration,
 highlighting potential management trade-offs for non-native species that
 may aid imperiled species recovery yet disrupt other native communities.
description: DRYAD_apparent.survival_movementDRYAD_nest.abundance.activity_season.lengthDRYAD_nest.DSRDRYAD_young.fledgedMetadata for DRYAD files
DOI: 10.5061/dryad.8h8q5
title: Data from: The Drosophila HNF4 nuclear receptor promotes glucose-stimulated insulin secretion and mitochondrial function in adults

description: Although mutations in HNF4A were identified as the cause of Maturity Onset
 Diabetes of the Young 1 (MODY1) two decades ago, the mechanisms by which
 this nuclear receptor regulates glucose homeostasis remain unclear. Here
 we report that loss of Drosophila HNF4 recapitulates hallmark symptoms of
 MODY1, including adult-onset hyperglycemia, glucose intolerance and
 impaired glucose-stimulated insulin secretion (GSIS). These defects are
 linked to a role for dHNF4 in promoting mitochondrial function as well as
 the expression of Hex-C, a homolog of the MODY2 gene Glucokinase. dHNF4 is
 required in the fat body and insulin-producing cells to maintain glucose
 homeostasis by supporting a developmental switch toward oxidative
 phosphorylation and GSIS at the transition to adulthood. These findings
 establish an animal model for MODY1 and define a developmental
 reprogramming of metabolism to support the energetic needs of the mature
 animal.
description: dHNF4_RNAseq_DiffExpr_1.5foldTotal RNA was extracted from dHNF4 mutants and genetically-matched control adult males (8 days old) using TriPure isolation reagent (Roche) followed by further purification/cleanup by RNeasy kit (QIAGEN). RNA from 4 biological replicates (n=40 flies per sample) per genotype was polyA-selected and assembled into barcoded libraries and pooled into a single-flow cell lane for Illumina HighSeq2000 50-cycle single-read sequencing, which produced ≥ 21.9 million reads per sample. Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly. Transcripts meeting a cutoff of ≥1.5 fold difference in mRNA abundance (~Log2 ≥ +/- 0.6) and FDR ≤ 1% were considered as differentially expressed genes. RNA quality control, library preparation, sequencing, and data analysis were performed at the University of Utah High Throughput Genomics and Bioinformatics Core Facilities.dHNF4_ChIPseq_NearestNeighbordHNF4-DNA bound complexes were immunoprecipitated using polyclonal antibody against endogenous dHNF4 protein. Barcoded libraries for dHNF4-IP and input control samples were generated by the University of Utah High Throughput Genomics core facility and sequenced in a single lane Illumina HiSeq 5-cycle single-read sequencing. Data analysis was performed by the Bioinformatics Core at the University of Utah School of Medicine using USeq and Model-based Analysis for ChIP-seq (MACS2) run with a peak shift of 100 bp. Enrichment peaks were identified with an FDR cutoff of 1% and nearest neighboring genes were compiled using USeq FindNeighboringGenes and UCSC dm3 EnsGenes gene tables. Nearest neighbor genes were compared to our RNA-seq dataset to identify neighbors that are also misexpressed in dHNF4 mutants, highlighting these as direct targets of dHNF4.
DOI: 10.5061/dryad.977cq
title: Data from: Taxonomic study on Japanese Salvia (Lamiaceae): Phylogenetic position of S. akiensis, and polyphyletic nature of S. lutescens var. intermedia

description: Both Salvia akiensis and S. lutescens (Lamiaceae) are endemic to Japan.
 Salvia akiensis was recently described in 2014 in the Chugoku (= SW
 Honshu) region, and each four varieties of S. lutescens distributed
 allopatrically. Among varieties in S. lutescens, var. intermedia show a
 disjunctive distribution in the Kanto (=E Honshu) and Kinki (= W Honshu)
 regions. Recent field studies of S. lutescens var. intermedia revealed
 several morphological differences between the Kanto and Kinki populations.
 Here, I evaluated these differences among Salvia lutescens var. intermedia
 and its allies with morphological analysis and molecular phylogenetic
 analyses of nuclear ribosomal DNA (internal and external transcribed
 spacer regions) and plastid DNA (ycf1-rps15 spacer, rbcL, and trnL-F)
 sequences. Both morphological analysis and molecular phylogenetic analyses
 showed that S. lutescens var. intermedia from the Kinki region and var.
 lutescens were closely related to each other. However, var. intermedia
 from the Kanto region exhibited an association with S. lutescens var.
 crenata and var. stolonifera, which also grew in eastern Japan, rather
 than var. intermedia in the Kinki region. These results indicated that S.
 lutescens var. intermedia is not a taxon with a disjunctive distribution,
 but a combination of two or more allopatric taxa. Present study also
 suggested that S. akiensis was most closely related to S. omerocalyx.
description: nrDNA
 DatasetConcatenated dataset of
 ETS+ITS DNA sequences of 36 Salvia taxa.nrDNAdataset
 Takano.fascpDNA
 DatasetConcatenated dataset of
 three plastid DNA (rbcL, trnL-F, ycf1-rps15) sequences of 36 Salvia
 taxa.cpDNAdataset
 Takano.fas
DOI: 10.5061/dryad.5qd036v
title: Data from: New Crystal Forms and Amorphous Phase of Sophoricoside: X-Ray Structures and Characterization

description: Sophoricoside, which is an isoflavone glycoside found in many plant
 species, has recently attracted attention because of its anti-fertility
 activity. One solvent-free form, two solvatomorphs and an amorphous phase
 of sophoricoside are reported for the first time. X-ray diffractometry,
 differential scanning calorimetry, thermal gravimetric analysis and
 Fourier-transform infrared spectroscopy were used to characterize the
 different forms. The results show that factors such as crystal symmetry,
 intermolecular arrangement, conformational flexibility, hydrogen-bonding
 interactions and solvent incorporation lead to different solid-state
 forms. An investigation of the transformations of the four forms showed
 that they can interconvert with each other under certain conditions.
 Amorphous phase and solvatomorphism were unstable but can improve the
 solubility of sophoricoside in water.
description: Raw data from “New
 crystal forms and amorphous phase of sophoricoside: X-ray structures and
 characterization”.PXRD analysis was
 performed using a D/max-2550 (Rigaku, Japan) X-ray diffractometer. Powders
 for PXRD were obtained by grinding crystalline materials in an agate
 mortar. The data were recorded in the angular range 3° to 40° (2θ) with a
 step size of 0.02° and scanning speed of 8° min−1. Simulated powder
 patterns were obtained using Mercury 2.4. The PXRD data were analyzed
 using JADE 6.5 software. DSC and TGA were performed with a Mettler-Toledo
 TGA/DSC STARe system (Mettler, Switzerland) under an atmosphere of dry N2
 flowing at 50 cm3 min−1. The TGA/DSC data were analyzed using STARe
 software. FT-IR absorption spectra were recorded with a Spectrum 400 FT-IR
 spectrophotometer (PerkinElmer, USA). The spectra were collected in the
 range 650 to 4000 cm−1 with a 4 cm−1 resolution. The FT-IR data were
 analyzed using SPECTRUM software.Sophoricoside.rar
DOI: 10.5061/dryad.j51h4
title: Data from: The efficiency of close inbreeding to reduce genetic adaptation to captivity

description: Although ex situ conservation is indispensable for thousands of species,
 captive breeding is associated with negative genetic changes: loss of
 genetic variance and genetic adaptation to captivity that is deleterious
 in the wild. We used quantitative genetic individual-based simulations to
 model the effect of genetic management on the evolution of a quantitative
 trait and the associated fitness of wild-born individuals that are brought
 to captivity. We also examined the feasibility of the breeding strategies
 under a scenario of a large number of loci subject to deleterious
 mutations. We compared two breeding strategies: repeated half-sib mating
 and a method of minimizing mean coancestry (referred to as gc/mc). Our
 major finding was that half-sib mating is more effective in reducing
 genetic adaptation to captivity than the gc/mc method. Moreover, half-sib
 mating retains larger allelic and adaptive genetic variance. Relative to
 initial standing variation, the additive variance of the quantitative
 trait increased under half-sib mating during the sojourn in captivity.
 Although fragmentation into smaller populations improves the efficiency of
 the gc/mc method, half-sib mating still performs better in the scenarios
 tested. Half-sib mating shows two caveats that could mitigate its
 beneficial effects: low heterozygosity and high risk of extinction when
 populations are of low fecundity and size and one of the following
 conditions are met: (i) the strength of selection in captivity is
 comparable with that in the wild, (ii) deleterious mutations are numerous
 and only slightly deleterious. Experimental validation of half-sib mating
 is therefore needed for the advancement of captive breeding programs.
description: Program code and
 resultsThe code of our
 simulations written in Delphi and Excel files with the results used in the
 manuscript's figuresmutdel+quanti.rar
DOI: 10.5061/dryad.5mb51
title: Data from: Deciphering information encoded in birdsong: male songbirds with fertile mates respond most strongly to complex, low-amplitude songs used in courtship

description: Research on the function of acoustic signals has focused on
 high-amplitude, long-range song (LRS) and largely ignored low-amplitude
 songs produced by many species during close-proximity, conspecific
 interactions. Low-amplitude songs can be structurally identical to LRS
 (soft LRS) or they can be widely divergent, sharing few spectral and
 temporal attributes with LRS (short-range song (SRS)). SRS is often more
 complex than LRS and is frequently sung by males during courtship. To
 assess function, we performed two playback experiments on males of a
 socially monogamous songbird. We compared responses of males whose mates
 were fertile or non-fertile to differences in song structure (SRS v. LRS
 and soft LRS), amplitude (SRS and soft LRS v. LRS), and tempo (slow v.
 fast SRS). Males responded more strongly to SRS than to LRS or soft LRS,
 indicating that song structure had a greater effect on response than song
 amplitude. SRS tempo did not detectably affect male response. Importantly,
 males responded more strongly to SRS when their mates were fertile,
 presumably because hearing SRS can indicate that a male's mate is
 being courted by an intruding male and a strong response can deter
 extra-pair competitors. We conclude that low-amplitude songs can function
 in both inter- and intra-sexual communication and should receive greater
 attention in future studies of mate choice and male-male competition.
description: Male behavioral response
 dataMale behavioral
 responses to song playbacks during their mate's fertile and
 non-fertile periods. Data are separated into pre-playback, playback, and
 post-playback observation periods.Reichardetal201X_AmNat_DryadSubmission.xmlReichardetal201X_AmNat_DryadSubmission.xls
DOI: 10.5061/dryad.19tb3dp
title: Data from: Belowground community responses to fire: meta-analysis reveals contrasting responses of soil microorganisms and mesofauna

description: Global fire regimes are shifting due to climate and land use changes.
 Understanding the responses of belowground communities to fire is key to
 predicting changes in the ecosystem processes they regulate. We conducted
 a comprehensive meta-analysis of 1634 observations from 131 empirical
 studies to investigate the effect of fire on soil microorganisms and
 mesofauna. Fire had a strong negative effect on soil biota biomass,
 abundance, richness, evenness, and diversity. Fire reduced microorganism
 biomass and abundance by up to 96%. Bacteria were more resistant to fire
 than fungi. Fire reduced nematode abundance by 88% but had no significant
 effect on soil arthropods. Fire reduced richness, evenness and diversity
 of soil microorganisms and mesofauna by up to 99%. We found little
 evidence of temporal trends towards recovery within 10 years
 post-disturbance suggesting little resilience of the soil community to
 fire. Interactions between biome, fire type, and depth explained few of
 these negative trends. Future research at the intersection of fire ecology
 and soil biology should aim to integrate soil community structure with the
 ecosystem processes they mediate under changing global fire regimes.
description: Extracted data from
 literature on soil organism responses to fireThe file contains data
 on soil organism biomass, abundance, richness, evenness, and diversity in
 burned and unburned soils extracted from peer reviewed publications
 published between 1988 and 2016 for use in meta-analysis. Soil organisms
 include bacteria, fungi, nematodes, protozoa, and arthropods. The file
 contains three sheets: (1) a read me file describing the contents of data
 sheets and columns therein; (2) a list of all published studies from which
 data was extracted for meta-analysis including first author, publication
 year, and journal; (3) a data file containing all data and accompanying
 information extracted from each publication. The contents of all columns
 are described in the ReadMe tab and file.Pressler_Oikos_MetaAnalysis_Data.xlsx
DOI: 10.5061/dryad.6th24
title: Data from: Extensive clonal spread and longevity of saw palmetto (Serenoa repens) provide insight into management plans

description: As an ecologically important foundation species, Serenoa repens provides
 crucial structural and functional services to many southeastern United
 States ecosystems. Its fruits are valuable to many vertebrates including
 medicinal uses by humans. Many land managers, however, consider Serenoa a
 troublesome plant that spread rapidly to dominate other plants.
 Accordingly, management plans have been developed to reduce Serenoa. Yet,
 we have little evidence of Serenoa spread/invasion. Furthermore, our
 understanding of its life history traits including generation time, clonal
 propagation, and seed recruitment is limited, which provides a poor basis
 for the development of proper management plans. By using AFLPs and
 clonal-network modeling, our goal is to reveal such life history
 information to provide insights into proper Serenoa management. We
 analyzed 263 Serenoa and 134 Sabal etonia (a sympatric non-clonal
 palmetto) samples collected from a 20 x 20 m plot in Florida scrub. Sabal
 samples were used to assign small palmettos whose species were
 unidentifiable in the field to Serenoa or Sabal and also as a negative
 control for clone detection. Our results suggest extensive clonal spread
 and remarkable longevity in Serenoa, while showing no evidence of Sabal
 clones. Serenoa predominantly propagate via vegetative sprouts and 10,000
 yr-old genets are likely common. The results of this and previous studies
 suggest that: (1) Serenoa has been part of scrub associations for
 thousands of years, (2) Serenoa invasion is unlikely, and (3) once reduced
 or eliminated from local communities, Serenoa’s restoration will be
 difficult. Reevaluation of the current management plans is an urgent task.
description: Dryad_Serenoa_263_177Dryad_Sabal_134_148
DOI: 10.5061/dryad.jv2m7q2
title: Data from: Locally and systemically induced glucosinolates follow optimal defence allocation theory upon root herbivory

description: 1. Herbivore-induced defences in plants are considered a strategy to
 manage multiple interactions while saving resources. The optimal defence
 theory (ODT) is one of the most prominent theoretical frameworks to
 explain the defence allocation patterns within plants. It was recently
 shown that the ODT generally applies to constitutive glucosinolate (GSL)
 allocation in shoot and root organs. Previous studies showed that both
 root and shoot herbivore feeding may alter defence allocation over plant
 organs. For shoots, the effect depends on where the herbivores feed. It is
 as yet unknown whether similar principles apply to root-herbivore induced
 GSLs. 2. To analyse the effects of root localized herbivore feeding on GSL
 allocation, we conducted a pot experiment using Anomala cuprea grubs and
 four Brassicaceae; Brassica rapa, B. nigra, B. oleracea, and Sinapis alba.
 Individuals of these four plant species were grown in dedicated mesocosms.
 The grubs were confined either to the bottom soil, the middle section, or
 to the top soil. Plants grown in the same set-ups but without root
 herbivores served as controls. Glucosinolate levels of the leaf lamina,
 petiole, and stem as well as of the taproot, lateral roots, and fine roots
 were measured after eight days of herbivory. 3. Plant biomass reduction
 due to herbivory was the largest when herbivores were confined to the top
 soil. In the three Brassica species, taproot GSL levels increased upon
 herbivory independent of where the root herbivores were feeding.
 Glucosinolate levels in fine roots and shoots, on the other hand, hardly
 responded to root herbivory. Indole GSLs, which are more effective to
 pathogens than to herbivores, were more strongly induced than aliphatic
 and aromatic GSLs, especially in the taproots. Sinapis alba did not show
 remarkable increments in any GSL level upon herbivory. 4. These results
 show that locally and systemically induced defences in roots are
 consistent with the ODT: the taproot which is the most vulnerable and
 valuable to plant performance shows the highest increase in defence
 induction. The induced GSL profiles suggest that the response may not only
 target herbivores, but may also help to prevent secondary infection by
 microbial pathogens.
description: Glucosinolate, plant
 biomass, and grub fresh weight data set.cosinolate, plant biomass, and
 grub fresh weight data set.coseAll data we used in our
 manuscript.Data.xlsx
DOI: 10.5061/dryad.1gn3b
title: Data from: Revisiting the pyrodiversity-biodiversity hypothesis: long-term fire regimes and the structure of ant communities in Neotropical savannas

description: 1. The idea that variable fire regimes (pyrodiversity) may increase
 habitat heterogeneity and, consequently, increase biodiversity at the
 landscape level is a relatively old one. However, this idea has been
 recently challenged by studies showing that the biota of fire-prone
 ecosystems is so resilient to fire that variation in fire regime has
 little ecological consequences. 2. We evaluated how communities of ants –
 a dominant faunal group – differ with variation in the frequency and
 seasonal timing of fire in Brazilian Cerrado (savanna), a global
 biodiversity hotspot. We compared the number and composition of ant
 species foraging on the ground and in trees among experimental treatments
 with three fire frequencies (unburned for 37 years and burned every 2 or 4
 years for the past 16 years) and three seasonal timings (early, mid and
 late dry season) of fire with a biennial frequency. 3. There were no
 significant differences in ant species richness in trees, and there were
 no significant differences in the richness of ground-dwelling ants among
 plots burned at different times of the dry season. However, unburned plots
 had fewer ground-dwelling ant species than those burned at 2 or 4 year
 intervals. We detected marked differences in species composition across
 regimes varying in both the frequency and the timing of fire, which were
 related to fire-induced changes in vegetation structure. Over 40% of the
 overall ant species richness recorded in our study site was attributed to
 differences in species composition among fire treatments. 4. Synthesis and
 applications. Our study shows that Cerrado ant diversity at the landscape
 scale is promoted by a diversity of fire regimes, and therefore supports
 the validity of the pyrodiversity–biodiversity hypothesis for the Cerrado
 biome. Our findings suggest that the current policy of fire suppression in
 Cerrado protected areas has a negative effect on overall biodiversity and
 therefore should be reconsidered.
description: Ground_Ants_Cerrado_Fire_2014Matrix of absolute frequency of each ground-dwelling ant species collected in 20 experimental fire plots.Tree_Ants_Cerrado_Fire_2014Matrix of absolute frequency of each tree-dwelling ant species collected in 20 experimental fire plots.