cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02v6wwq0w
title: Data from: Phylogenomics, biogeography, and evolution of the blue- or white-fruited dogwoods

description: In this study, we combined data from RAD-seq, morphology, fossils, and
 ecological niche to understand species relationships, biogeographic
 history, ecological niche and morphological evolution of the blue- or
 white-fruited dogwoods, the largest of the four major clades of Cornus.
 Our phylogenomic analyses with RAxML and MrBayes recovered a strongly
 supported and well-resolved phylogeny of the BW group with three
 intercontinental disjunct clades in east Asia/Eurasia and North America -
 of which two in subg. Kraniopsis are newly identified. Divergence time
 analyses with BEAST and treePL and DEC-based total evidence analysis
 resolved an ancestral range of the BW crown in eastern Asia or Eurasia in
 the Late Cretaceous and ancestral ranges of the three disjunct clades in
 Eurasia and North America during the Miocene, suggesting dispersal via the
 North Atlantic and Bering land bridges. Character mapping and comparison
 of ecological niche, morphospace, and rate of evolution shows evidence of
 different divergence patterns in morphology, ecological niche, and
 molecules of the disjunct sisters. The overall diversity bias towards EA
 cannot be explained by a greater net diversification rate but rather an
 early diversification of subg. Kraniopsis in EA. Although morphological
 stasis was observed in most of the characters across the disjuncts,
 evolutionary changes in vegetative, fruit, and habit traits may be
 attributed to continental differences in temperature, precipitation, and
 elevation. These findings in conjunction with previous studies suggest the
 EA-ENA disjunct floras are an assembly of lineages descended from the
 boreotropical or mesophytic flora through taxon-specific evolutionary
 pathways.
DOI: 10.7272/q6bg2m6w
title: Results of a Person-Centered Maternal Health Quality Improvement intervention in Uttar Pradesh, India

description: This data is from a larger 5 year project on
 person-centered quality for delivery, family planning, and abortion in
 both India and Kenya. We conducted a quality improvement collaborative to
 improve person-centered quality for maternal health services in Uttar
 Pradesh, India. Data was collected pre and post
 intervention. The aim was to evaluate if quality improvement
 cycles were effective at improving women's experiences while
 seeking care and if the changes made during this intervention could be
 spread to other facilities.
description: Data was collected through a series of survey interviews with
 providers and post-partum maternity patients at government health
 facilities in Uttar Pradesh, India.  The surveys were conducted over three
 years beginning in 2016
description: We have redacted locale information from both survey instruments
 and datasets, along with indentifiers of any related geographic
 information.  We believe all other needed data is both included in the
 dataset, and can be understood using the materials included.
DOI: 10.7280/d1nh4w
title: Data from: In-vitro cultivation of liveforevers (genus Dudleya) to reduce poaching and extinction

description: The genus Dudleya consists of many rare and endangered species. Recently,
 poaching has emerged as a critical threat to the continued survival of
 these plants in the wild. Conservationists will typically store seeds and
 grow new plants, but this method could limit propagation if viability and
 seed availably is unreliable. Nursery growing efforts have been limited by
 unreliable and scarce seed sources, and challenges to maintaining
 genetically isolated populations, as Dudleya species readily hybridize.
 Micropropagation can overcome these challenges by exponentially cloning
 plants to deflate poaching incentives. This project made progress toward
 developing an aseptic culture method of propagation of Dudleya, meaning
 growing plants in a sterile growing environment. First, I compared the
 propagation of in-vitro and ex-vitro grown seeds to understand if in-vitro
 culture enhances germination, survival, and growth. Second, I compared
 nine decontamination protocols to determine which one is in better at
 minimizing microbial contamination and damage to plant
 tissue. For seeds, the germination rate varied among treatments
 and species. Plants grew larger ex-vitro (in the greenhouse), but
 experienced mortality, whereas all seedlings survived in-vitro (in
 culture). For cuttings, I found that NaDCC (sodium dichloroisocyanura)
 resulted in less contamination and necrosis than bleach. An effective
 method of applying NaDCC was identified to introduce rare cuttings of
 select Dudleya species into in-vitro culture. This research provides a
 foundation for conservationists to continue to optimize the
 micropropagation process, and also provides an effective tool for
 germplasm storage.
DOI: 10.5061/dryad.9w0vt4bc6
title: Data from: Life history variation in an invasive plant is associated with climate and recent colonization of a specialist herbivore

description: Premise: Spatial variation in selective pressures can lead to
 intraspecific variation in life history, favoring some life histories and
 constraining others depending on the vulnerability of life stages. We
 examined how spatial variation in herbivory and climate influences
 flowering size and the occurrence of semelparity (reproducing once) versus
 iteroparity (reproducing multiple times) in the introduced range of an
 invasive plant, houndstongue (Cynoglossum officinale). Houndstongue is a
 short-lived semelparous perennial in its native range. In its introduced
 range, we previously documented increased rates of iteroparity and a
 higher median threshold flowering size compared to the native range. We
 hypothesized that the recent introduction of a specialist biocontrol
 insect (a root-boring weevil, Mogulones crucifer) would decrease threshold
 flowering size, and reduce the proportion of iteroparous plants, because
 M. crucifer preferentially attacks large individuals and may reduce
 overwinter survival. Methods: We surveyed 24 sites across the northwestern
 United States to quantify the frequency of semelparity versus iteroparity
 and to estimate weevil abundance, and used demographic data collected from
 six sites to estimate median threshold flowering size. Key Results: We
 found that sites with greater winter precipitation and no weevils had a
 greater proportion of iteroparous plants. Sites with higher weevil attack
 had a lower median threshold flowering size. Conclusions: The variation in
 frequency of flowering and threshold flowering size that we documented in
 North American houndstongue populations and the relationships between this
 variation and herbivory and climate provide evidence for how selective
 pressures covary with the life histories of invasive plants.
description: Please see Methods in paper for details of data collection and
 processing.
description: See ReadMe file for description of data.
DOI: 10.5061/dryad.vdncjsxr6
title: Data from: Agricultural adaptation in the native North American weed waterhemp, Amaranthus tuberculatus (Amaranthaceae)

description: There is increasing interest in documenting adaptation of weedy plant
 species to agricultural ecosystems, beyond the evolution of herbicide
 resistance. Waterhemp (Amaranthus tuberculatus) is a native plant of the
 Midwestern U.S. that began infesting agricultural fields in the 20th
 century within the central portion of its range. We hypothesized that the
 vegetative growth and reproductive traits of waterhemp from this heavily
 infested central region provide differential fitness benefits in
 agricultural environments. We collected seeds from across the
 species’ native range, representing regions with varying degrees of
 waterhemp infestation, and planted them together in common garden soybean
 plots. A 2010 common garden experiment was conducted within the range of
 agriculturally weedy waterhemp (in Missouri), and a 2011 common garden
 experiment was conducted outside of this range (in Ohio). Days to
 flowering and flowering plant height, mature plant size data (height,
 number of branches, and length of the longest branch), and above-ground
 biomass were measured to estimate relative fitness. In both common garden
 locations, plants from regions where waterhemp occurs as an agricultural
 weed — including those from the heavily infested Mississippi Valley region
 (Iowa, Illinois, and Missouri) and the less severely infested Plains
 region (Nebraska, Kansas, and Oklahoma) — had higher relative performance
 in almost all fitness-related measures than plants from the Northeast
 region (Ohio, Michigan, and Ontario), which had little to no
 agriculturally weedy waterhemp at the time of our study. Further analysis
 revealed that fewer days to flowering in the Northeast populations can be
 largely accounted for by latitude of origin, suggesting a strong genetic
 influence on this reproductive trait. These findings suggest intraspecific
 variation in agricultural adaptation in a native U.S. weed, and support
 the use of agricultural weeds to study adaptation.
description: This dataset was collected from field-grown plants grown in
 common gardens in 2010 and 2011. It has been filtered to exclude plants
 with missing data or other problems, as detailed in the
 Supporting Information Methods of the manuscript.
description: Note the README file.
DOI: 10.5061/dryad.kh1893236
title: Data from: Profiling extracellular long RNA transcriptome in human plasma and extracellular vesicles for biomarker discovery

description: The recent discovery of extracellular RNAs in blood, including RNAs in
 extracellular vesicles (EVs), combined with low-input RNA-sequencing
 advances have enabled scientists to investigate their role in human
 disease. To date, most studies have been focusing on small RNAs, and
 methodologies to optimize long RNAs measurement are lacking. We used
 plasma RNA to assess the performance of six long RNA sequencing methods,
 at two different sites, and we report their differences in reads (%)
 mapped to the genome/transcriptome, number of genes detected, long RNA
 transcript diversity, and reproducibility. Using the best performing
 method, we further compare the profile of long RNAs in the EV- and
 no-EV-enriched RNA plasma compartments. These results provide insights on
 the performance and reproducibility of commercially available kits in
 assessing the landscape of long RNAs in human plasma and different
 extracellular RNA carriers that may be exploited for biomarker discovery.
description: Tarball with raw counts and transcript TPMs for the library kits
 tested, and the vesicle isolations tested in the accompanying
 manuscript: countTable_libraryKits.csv<br>
 tpmTable_libraryKits.csv<br> countTable_vesicles.csv<br>
 tpmTable_vesicles.csv
DOI: 10.5061/dryad.w3r2280n6
title: Isolation by geographical distance after release from Pleistocene refugia explains genetic and phenotypic variation in Xylotrupes siamensis (Coleoptera: Scarabaeidae)

description: Consistent and objective species delimitation is crucial to biodiversity
 studies, but challenges remain when conflicting taxonomic decisions have
 been made because different data sets and analytical methods were used to
 delineate species. In the rhinoceros beetle, Xylotrupes siamensis, the use
 of different morphological characters has resulted in taxonomic
 disagreement between studies. We used three molecular loci (mitochondrial
 CO1 and nuclear ITS2 and H3) to investigate the genetic divergence between
 populations exhibiting different male horn phenotypes. We also applied an
 approximate Bayesian computation approach to test alternative historical
 hypotheses that might explain the present genetic diversity among
 geographical populations. Furthermore, we used species distribution models
 to estimate the temporal variation in the geographical distribution of
 suitable habitats. The results show that the two phenotypic taxa within X.
 siamensis are not genetically structured and that their genetic structure
 can be explained using isolation by geographical distance. The emergence
 of the two phenotypic taxa might have been associated with historical
 isolation in separate refugia. However, spatial expansion and genetic
 interchange between populations might have gradually eroded the spatial
 genetic structure. We demonstrate that understanding the historical
 processes responsible for phenotypic divergence and genetic diversity
 among current populations could help with making evolutionarily coherent
 taxonomic decisions.
DOI: 10.5061/dryad.sf7m0cg3g
title: Data from: Plant communities, populations and individuals have distinct responses to short-term warming and neighbour biomass removal in two montane grasslands

description: Aims Climate change will impact plant communities and populations but also
 individual plant performance. Most predictive models of community
 responses to climate change ignore individual‐level biotic interactions
 despite their known importance for community diversity and functioning.
 Here, we consider plant fitness and diversity responses to climate change
 associated factors at three organisational levels: communities,
 populations and individual plants, to increase our understanding of how
 plant communities respond to climate change. Location Montane grassland,
 Tasmania, Australia. Methods In two plant communities, we manipulated
 temperature using open‐top chambers and removed random and dominant
 species biomass. Two years after experimental manipulations, we assessed
 the impact of treatments on species diversity, community‐ and
 population‐level functional traits and individual plant fitness. Results
 Species diversity was affected by warming in one of the two communities,
 while community‐level functional trait diversity metrics were unaffected
 by treatments. Mean community trait values were strongly impacted by
 dominant species biomass removal in both communities, notably increasing
 specific leaf area (SLA) and specific root length. SLA showed the
 strongest population‐level trait response, with higher values found in
 warmed plots and lower values found in dominant species biomass removal
 plots. Neighbours had a stronger competitive effect on individual plant
 fitness in warmed compared to unwarmed conditions at the higher‐elevation
 site and facilitation was common in both communities. Conclusions We
 demonstrated that over short time scales, plant communities respond to
 experimental warming and biomass removal across multiple organisational
 levels. Competitive and facilitative interactions played a significant
 role in determining fitness outcomes, but competitive interactions
 dominated under warmed conditions. We highlight the importance of
 local‐scale biotic interactions in mediating individual responses to
 warming and recommend their inclusion in future studies of how climate
 change will impact the long‐term structure and function of plant
 communities through short‐term impacts on individual plant fitness.
description: Data were collected in two montane grassland sites in Tasmania,
 Australia, in a factorial experiment where the temperature was manipulated
 using open-top chambers, and random and dominant species biomass were
 removed. Data were collected at organisational levels: 1) community
 (composition and trait data), 2) population (trait data) and 3) individual
 (fecundity).
description: The first sheet contains community composition data for each plot
 and the second worksheet is the community trait data. The third and fourth
 worksheets are the population-level trait data and individual fecundity
 data. ReadMe (metadata) information for each worksheet is provided in the
 fifth worksheet.
DOI: 10.5061/dryad.jq2bvq86r
title: Data from: Theta oscillations coincide with sustained hyperpolarization in CA3 pyramidal cells, underlying decreased firing

description: Brain-state fluctuations modulate membrane potential dynamics of neurons,
 influencing the functional repertoire of the network. Pyramidal cells
 (PCs) in hippocampal CA3 are necessary for rapid memory encoding,
 preferentially occurring during exploratory behavior in the
 high-arousal theta state. However, the relationship between the
 membrane potential dynamics of CA3 PCs and theta has not been
 explored. Here, we characterize the changes in the membrane potential
 of  PCs in relation to theta using electrophysiological
 recordings in awake mice. During theta, most PCs behave in a
 stereotypical manner, consistently hyperpolarizing time-locked to the
 duration of  theta. Additionally, PCs display lower membrane
 potential variance and reduced firing rate. In contrast, during
 large irregular activity, a low-arousal state, PCs show heterogeneous
 changes in membrane potential. This suggests coordinated
 hyperpolarization of PCs during theta, possibly caused by
 increased inhibition. This could lead to higher signal-to-noise ratio in
 the small population of PCs active during theta as observed in
 ensemble recordings.
description: To investigate the intracellular dynamics of hippocampal CA3
 pyramidal cells (PCs) in vivo across brain states, we
 performed simultaneous whole-cell and local field potential (LFP)
 recordings in awake head-fixed mice free to run on a wheel. An LFP
 electrode was first positioned in the stratum pyramidale of dorsal CA3
 before lowering the patch-clamp electrode for whole-cell recordings in the
 vicinity of the LFP electrode.  To monitor the level of arousal, we
 measured both pupil diameter and locomotor activity on the wheel. We
 recorded a total of 33 CA3 PCs in 21 mice. For details
 about how these raw data were processed to produce the provided dataset,
 please see https://github.com/Ashkees/Malezieux_CellRep_2020 For more information about data collection and processing, please see the corresponding paper.
description: Files: README provides instructions for how to
 use this dataset Malezieux_CellRep.xlsx provides some
 metadata
DOI: 10.5061/dryad.d51c5b007
title: Data from: Biocultural approaches to sustainability: a systematic review of the scientific literature

description: Current sustainability challenges demand approaches that acknowledge a
 plurality of human-nature interactions and worldviews, for which
 biocultural approaches are considered appropriate and timely. This
 systematic review analyses the application of biocultural approaches to
 sustainability in scientific journal articles published between 1990 and
 2018 through a mixed methods approach combining qualitative content
 analysis and quantitative multivariate methods. The study identifies seven
 distinct biocultural lenses, i.e. different ways of understanding and
 applying biocultural approaches, which to different degrees consider the
 key aspects of sustainability science - inter and transdisciplinarity,
 social justice and normativity. The review suggests that biocultural
 approaches in sustainability science need to move from describing how
 nature and culture are co-produced to co-producing knowledge for
 sustainability solutions, and in so doing, better account for questions of
 power, gender and transformations, which has been largely neglected thus
 far.
description: Data collection and processing are described in the main
 manuscript and the supplementary information.
description: A detailed description of the individual variables can be found
 in the main manuscript and the supplementary information. There are no
 missing values.
DOI: 10.5061/dryad.d7wm37pzc
title: Data from: Bacterial phylogeny predicts volatile organic compound composition and olfactory response of an aphid parasitoid

description: There is increasing evidence that microorganisms emit a wide range of
 volatile compounds (mVOCs, microbial volatile organic compounds) that act
 as insect semiochemicals, and therefore play an important role in insect
 behaviour. Although it is generally believed that phylogenetically closely
 related microbes tend to have similar phenotypic characteristics and
 therefore may elicit similar responses in insects, currently little is
 known about whether the evolutionary history and phylogenetic
 relationships among microorganisms have an impact on insect-microbe
 interactions. In this study, we tested the hypothesis that phylogenetic
 relationships among 40 Bacillus strains isolated from diverse
 environmental sources predicted mVOC composition and the olfactory
 response of the generalist aphid parasitoid Aphidius colemani. Results
 revealed that phylogenetically closely related Bacillus strains emitted
 similar blends of mVOCs and elicited a comparable olfactory response of A.
 colemani in Y-tube olfactometer bioassays, varying between attraction and
 repellence. Analysis of the chemical composition of the mVOC blends showed
 that all Bacillus strains produced a highly similar set of volatiles, but
 often in different concentrations and ratios. Benzaldehyde was produced in
 relatively high concentrations by strains that repel A. colemani, while
 attractive mVOC blends contained relatively higher amounts of acetoin,
 2,3-butanediol, 2,3-butanedione, eucalyptol and isoamylamine. Overall,
 these results indicate that bacterial phylogeny had a strong impact on
 mVOC compositions and as a result on the olfactory responses of insects.
DOI: 10.5061/dryad.vhhmgqnqv
title: Dataset for group living and duetting in barbet species

description: The duets of birds have intrigued biologists for a long time, yet much
 remains unknown about the evolution of these striking collective displays.
 This is because previous studies on duet evolution have been biased to
 songbirds and neglected other bird groups. In songbirds, the absence of
 migration has been found to predict the occurrence of duetting, indirectly
 supporting the idea that duet communication is linked with pair-bonding.
 Here, we used phylogenetic comparative analyses in a sedentary clade of
 non-songbirds, the barbets (Capitonidae), to reveal new correlates of duet
 evolution in birds. We found (1) that duets evolved several times
 independently in different barbet lineages and (2) that duetting evolved
 in association with group living (i.e. the presence of helpers or
 non-breeding adults during the breeding period), but not with sexual
 monochromatism or habitat type. We conclude that the evolution of social
 systems has a major influence on the evolution of collective signalling
 such as duetting. When social living causes resource competition among
 group members or increases the risk of paternity loss, duetting by primary
 pairs would play a key role in signalling mate guarding and dominance
 against subordinate group members.
description: We collected information on the presence/absence of duets for
 each species of the family Capitonidae from pubished literatures, and the
 web-based sound library Xeno-Canto (http://www.xeno-canto.org). Informatin
 on body size, habitat, and sociality was also collected based on published
 literatures.