cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1ns1rn8x3
title: Habitat loss increases seasonal interaction rewiring in plant-pollinator networks

description: Understanding the flexibility of interactions and network rewiring (i.e.
 reassembly of interactions due to partner-switching) is necessary to
 comprehend how future anthropogenic changes will affect interspecific
 interactions and the functioning of communities. A higher rewiring could
 be expected in more disturbed landscapes because these landscapes contain
 fewer and more generalist species with more homogeneous traits. We sampled
 pollination interactions in 20 wild Olea europaea communities along a
 disturbance gradient to evaluate the hypothesis that the loss of natural
 habitats increases seasonal (within-year) interaction rewiring in
 plant-pollinator communities, influencing their functional structure. For
 this, we particularly tested whether rewiring frequency was negatively
 related to the extent of natural habitats surrounding the communities,
 whether interaction rewiring influenced the static structure of networks
 (nestedness, network specialization –H2’–), and whether a high
 generalization (low specialization –d’–) and abundance of species in
 communities made them more prone to rewiring. We show that habitat loss
 increased seasonal interaction rewiring in networks. Changes in rewiring
 were related to changes in the cumulative static structure of pollination
 networks. Nestedness decreased and network specialization (H2’) also
 tended to decrease as interaction rewiring increased, suggesting an
 indirect effect of habitat loss on the robustness of networks through
 their dynamics. As expected, generalist insect and plant species were more
 prone to rewiring. However, flower abundance had different effects on the
 rewiring probability of plant species depending on the extent of habitat
 loss, with abundant species rewiring more in disturbed communities and
 rewiring less in more natural communities. Likely, this is related to the
 context-dependent foraging behaviour of pollinators, which may switch to
 more abundant species if the cost of searching for trait-matching
 resources is high in disturbed habitats. Our work shows the role of
 partner-switching in generalist species to adapt to new conditions. It
 also highlights the importance of going beyond general network metrics to
 understand the underlying processes of community-level interaction
 assembly, and predict and anticipate the effects of anthropogenic
 disturbances on pollination services.
DOI: 10.5061/dryad.dncjsxm34
title: Latent Transforming Growth Factor β Binding Protein 3 Controls Adipogenesis

description: Transforming growth factor-beta (TGFβ) is released from cells as part of a
 trimeric latent complex consisting of TGFβ, the TGFβ propeptides, and
 either a latent TGFβ binding protein (LTBP) or glycoprotein-A
 repetitions predominant (GARP) protein. LTBP1 and 3 modulate
 latent TGFβ function with respect to secretion, matrix localization, and
 activation and, therefore, are vital for the proper function of the
 cytokine in a number of tissues. TGFβ modulates stem cell differentiation
 into adipocytes (adipogenesis), but the potential role of LTBPs in this
 process has not been studied. We observed that 72 h post adipogenesis
 initiation Ltbp1, 2, and 4 expression
 levels decrease by 74-84%, whereas Ltbp3 expression
 levels remain constant during adipogenesis. We found that LTBP3 silencing
 in C3H/10T1/2 cells reduced adipogenesis, as measured by the percentage of
 cells with lipid vesicles and the expression of the transcription factor
 peroxisome proliferator-activated receptor gamma
 (PPARγ). Lentiviral mediated expression of
 an Ltbp3 mRNA resistant to siRNA targeting rescued the
 phenotype, validating siRNA specificity. Knockdown (KD)
 of Ltbp3 expression in 3T3-L1, M2, and primary bone
 marrow stromal cells (BMSC) indicated a similar requirement
 for Ltbp3. Epididymal and inguinal white adipose tissue fat pad
 weights of Ltbp3-/- mice were reduced by 62% and 57%,
 respectively, compared to wild-type mice. Inhibition of
 adipogenic differentiation upon LTBP3 loss is mediated by TGFβ, as TGFβ
 neutralizing antibody and TGFβ receptor I kinase blockade rescue the LTBP3
 KD phenotype. These results indicate that LTBP3 has a TGFβ-dependent
 function in adipogenesis both in vitro and possibly in vivo.
description: Please look at the method section of the manuscript.
description: Excel
DOI: 10.5061/dryad.jq2bvq8cg
title: Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution

description: Examples of parallel evolution have been crucial for our understanding of
 adaptation via natural selection. However, strong parallelism is not
 always observed even in seemingly similar environments where natural
 selection is expected to favour similar phenotypes. Leveraging this
 variation in parallelism within well-researched study systems can provide
 insight into the factors that contribute to variation in adaptive
 responses. Here we analyze the results of 36 studies reporting 446 average
 trait values in Trinidadian guppies, Poecilia reticulata, from different
 predation regimes. We examine how the extent of predator-driven phenotypic
 parallelism is influenced by six factors: sex, trait type, rearing
 environment, ecological complexity, evolutionary history, and time since
 colonization. Analyses show that parallel evolution in guppies is highly
 variable and weak on average, with only 24.7% of the variation among
 populations being explained by predation regime. Levels of parallelism
 appeared to be especially weak for colour traits, and parallelism
 decreased with increasing complexity of evolutionary history (i.e., when
 estimates of parallelism from populations within a single drainage were
 compared to estimates of parallelism from populations pooled between two
 major drainages). Suggestive – but not significant – trends that warrant
 further research include interactions between the sexes and different
 trait categories. Quantifying and accounting for these and other sources
 of variation among evolutionary “replicates” can be leveraged to better
 understand the extent to which seemingly similar environments drive
 parallel and nonparallel aspects of phenotypic divergence.
DOI: 10.5061/dryad.pk0p2ngrc
title: Yellow creek abundance data for stream fish response to drought

description: Climate change projections in the western United States suggest that
 snowpack levels and winter precipitation will decline, but mean annual
 precipitation levels will remain unchanged. Mountain streams that once saw
 a constant source of water from snowpack will begin to see large seasonal
 variation in flow. Increased stream intermittency will create significant
 conservation risks for fish species; however, few studies have examined
 the abundance responses of fish in high elevation streams to the shift
 from perennial to intermittent flow. To determine the effects of stream
 intermittency on fish abundance in a montane stream, we quantified changes
 in abundance for five species over a five-year period that exhibited
 extreme variation in streamflow. Responses varied by species and life
 stage, suggesting that the shift from perennial to intermittent flow will
 cause significant declines in abundance for some species. Northern
 leatherside chub, may experience large decreases in their range as the
 availability of perennial streams decreases. The study of drought effects
 on fish abundance will be crucial to the conservation of biodiversity in
 montane regions of the world.
description: We estimated numbers of individuals for each species, using a
 backpack electroshocker with standard electrofishing procedures. We used
 block nets to provide closure at the ends of the segment during years when
 the stream reach was flowing. We used a two-pass removal depletion method
 to estimate abundances within segments. After placing captured fish in
 aerated coolers filled with stream water, we identified fish to species
 and categorized them by life stage (juvenile or adult) based on standard
 length, and then returned the fish to the same section of stream. In 2011
 (the first year), size data for R. balteatus were only available for the
 first 30 fish caught (sampling in 2011 was focused mainly on R. osculus,
 and L. copei, for a mark-recapture study that is reported elsewhere).
 However, we recorded number captured of R. balteatus for each segment and
 pass of the stream reach. We calculated the ratio of adult to juvenile
 life stages of the first 30 fish, and used that ratio to estimate the R.
 balteatus life stage distribution (adult or juvenile) for additional
 segments for 2011 only. To estimate abundances, we used a
 maximum-likelihood population estimator (Microfish, Van Deventer 1998).
 The data has been given both as the estimate generated by the
 maximum-likelihood population estimate, as well as a log transformed
 version of the original estimate. 
description: Data is provided in a .xlsx file. It can be opened on Excel,
 Google Sheets, or Apple Numbers.
DOI: 10.5061/dryad.p5hqbzks7
title: Geographic range size, water temperature and extrinsic threats predict the extinction risk in global cetaceans

description: Despite that cetaceans provide significant ecological contributions to the
 health and stability of aquatic ecosystems, they are highly endangered
 with nearly one-third of species assessed as threatened with extinction.
 Nevertheless, to date, few studies have explicitly examined the patterns
 and processes of extinction risk and threats for this taxon, and even less
 between the two subclades (Mysticeti and Odontoceti). To fill this gap, we
 compiled a dataset of six intrinsic traits (active region, geographic
 range size, body weight, diving depth, school size and reproductive
 cycle), six environmental factors relating to sea surface temperature and
 chlorophyll concentration, and two human-related threat indices that are
 commonly recognized for cetaceans. We then employed phylogenetic
 generalized least square (PGLS) models and model selection to identify the
 key predictors of extinction risk in all cetaceans, as well as in the two
 subclades. We found that geographic range size, sea surface temperature
 and human threat index were the most important predictors of extinction
 risk in all cetaceans and in odontocetes. Interestingly, maximum body
 weight was positively associated with the extinction risk in mysticetes,
 but negatively related to that for odontocetes. By linking seven major
 threat types to extinction risk, we further revealed that fisheries
 bycatch was the most common threat, yet the impacts of certain threats
 could be overestimated when considering all species rather than just
 threatened ones. Overall, we suggest that conservation efforts should
 focus on small-ranged cetaceans and species living in warmer waters or
 under strong anthropogenic pressures. Moreover, further studies should
 consider the extinction risk of species when superimposing risk maps and
 quantifying risk severity. Finally, we emphasize that mysticetes and
 odontocetes should be conserved with different strategies, because their
 extinction risk patterns and major threat types are considerably
 different. For instance, large-bodied mysticetes and small-ranged
 odontocetes require special conservation priority.
DOI: 10.5061/dryad.6djh9w143
title: Data from: Across space and time: a review of sampling and analytical biases in fossil data across macroecological scales

description: Quantitative studies of fossil data have proven critical to a number of
 major macroevolutionary and macroecological discoveries, such as the ‘Big
 5’ mass extinctions of the Phanerozoic. The development and easy
 accessibility of major meta-data sources such as the Paleobiology Database
 and Geobiodiversity Database have also spurred the widespread application
 of these data to testing ecological hypotheses at finer spatiotemporal and
 phylogenetic scales. However, issues of preservational/taphonomic biases,
 sampling/collecting biases, taxonomic issues, and analytical choice can
 impact the degree of interpretative resolution possible, and even obscure
 biological ‘signal’ from error/bias-introduced ‘noise’. The degree to
 which these factors can impact analytical interpretations is not
 well-documented in comparison to the scale of use of these data sources.
 Here, we review the many forms of systematic error that can creep into a
 paleoecological study, from the stage of data collection to the
 interpretation of analytical results, and provide two case studies based
 upon re-analysis of previously-published datasets to illustrate the
 varying impacts of such biases. The first case study focuses on the
 Cambrian Burgess Shale, and the second on the Belly River Group, with both
 representing highly-sampled, taphonomically characterized, and
 spatiotemporally-constrained datasets developed through multiple years of
 sustained field collecting. In the former, we illustrate the impacts of
 collecting bias through quantitative comparisons of collected vs.
 discarded specimens over multiple field seasons, illustrating the impact
 of this data loss on ecological reconstructions and analysis. In the
 latter case study, we review the impact of preservational biases, the
 approaches to their quantification and mitigation, where these approaches
 have led to misinterpretations in the past, and the differences in
 ecological resolution that result from occurrence vs abundance approaches
 in macroecological analysis. Lastly, we synthesize these case studies with
 our review of past approaches to propose a series of recommendations for
 future paleoecological and macroecological studies, emphasizing the
 continued importance of high-quality primary data and ongoing need for a
 first-principles approach to address existing issues of missing data.
DOI: 10.15468/dl.ah4gh2
title: Occurrence Download

description: A dataset containing 239 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fraxinus bungeana"
 ]
}

 The dataset includes 239 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003210-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h9w0vt4mp
title: Data and scripts from: Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia

description: The microbial community composition is crucial for diverse life-history
 traits in many organisms. However, we still lack
 a sufficient understanding of how the host microbiome is
 acquired and maintained, a pressing issue in times of global environmental
 change. Here we investigated to what extent host genotype, environmental
 conditions, and the endosymbiont Wolbachia influence the
 bacterial communities in the parasitic wasp Asobara japonica. We
 sampled multiple wasp populations across ten locations
 in their natural distribution range in Japan and sequenced the host genome
 (whole genome sequencing) and microbiome (16S rRNA gene). We compared the
 host population structure and bacterial community composition of wasps
 that reproduce sexually and are uninfected
 with Wolbachia with wasps that reproduce asexually and
 carry Wolbachia. The bacterial communities in asexual wasps were
 highly similar due to a strong effect
 of Wolbachia rather than host genomic structure. In
 contrast, in sexual wasps, bacterial communities appear primarily shaped
 by a combination of population structure and environmental conditions. Our
 research highlights that multiple factors shape the bacterial communities
 of an organism and that the presence of a single endosymbiont can strongly
 alter their compositions. This information is crucial to understanding how
 organisms and their associated microbiome will react in the face of
 environmental change.
description: A detailed description of how
 samples were collected, processed, and analysed can be found in the
 publication: Brinker et al. 2022, Microbiome composition is shaped by
 geography and population structure in the parasitic wasp <em>Asobara
 japonica</em>, but not in the presence of the endosymbiont
 <em>Wolbachia</em>.
DOI: 10.15468/dl.je8crq
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((5.91246 43.89781,5.87129 43.87363,5.88349 43.86483,5.94754 43.85604,6.1229 43.89341,6.24184 43.92966,6.32723 43.87693,6.37145 43.84394,6.44922 43.87583,6.46295 43.91868,6.466 43.99662,6.41568 44.07007,6.3684 44.09636,6.27539 44.035,6.19762 44.01746,6.13357 43.98345,6.07563 43.94613,5.99786 43.91429,5.91246 43.89781))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Symphyotrichum salignum"
 ]
}

 The dataset includes 19 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003215-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4qrfj6qd4
title: Gene expression underlying parenting and being parented shows limited plasticity in response to different ambient temperatures

description: Flexible interactions between parents and offspring are essential for
 buffering families against variable, unpredictable, and challenging
 environmental conditions. In the subsocial carrion beetle, Nicrophorus
 orbicollis, mid-summer temperatures impose steep fitness costs on parents
 and offspring but do not elicit behavioral plasticity in parents. Here, we
 ask if plasticity of gene expression underpins this behavioral stability
 or facilitates independent compensation by larvae. To test this, we
 characterized gene expression of parents and offspring before and during
 active parenting under benign (20°C) and stressful (24°C) temperatures to
 identify genes of parents and offspring associated with thermal response,
 parenting/being parented, and gene expression plasticity associated with
 behavioral stability of parental care. The main effects of thermal and
 social condition each shaped patterns of gene expression in females,
 males, and larvae. In addition, we implicated 79 genes in females as
 ‘buffering’ parental behavior across environments. The majority of these
 underwent significant changes in expression in actively parenting mothers
 at the benign temperature, but not at the stressful temperature. Our
 results suggest that neither genetic programs for parenting nor their
 effects on offspring gene expression are fundamentally different under
 stressful conditions, and that behavioral stability is associated
 primarily with the maintenance of existing genetic programs rather than
 replacement or supplementation. Thus, while selection for compensatory
 gene expression could expand the range of thermal conditions parents will
 tolerate, without expanding the toolkit of genes involved selection is
 unlikely to lead to adaptive changes of function.
description: DNA was extracted from the heads and full bodies of adult and
 larval burying beetles, respectively, in a 3 x 2 x 2 factorial design: 3
 family members (males, females, larvae), 2 thermal conditions (20°C
 and 24°C),
 and 2 social conditions (before and during parenting/being parented).
 Transcripts were filtered and quantified using StringTie and all
 subsequent analysis steps were performed in R. 
description: This analysis uses the free programming software, R, along with
 the following packages: plyr
 dplyr data.table
 magrittr countToFPKM #version 1.0 https://cran.r-project.org/web/packages/countToFPKM/index.html qdapRegex IsoformSwitchAnalyzeR DESeq2 ballgown pcaExplorer factoextra VennDiagram RRHO RRHO2 topGO GOplot genefilter devtools smatr
DOI: 10.15468/dl.h8hde2
title: Occurrence Download

description: A dataset containing 689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pedicularis spicata"
 ]
}

 The dataset includes 689 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003212-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2fqz612s8
title: Microtubule retrograde flow retains neuronal polarization in a fluctuating state

description: In developing vertebrate neurons, a neurite is formed by more than a
 hundred microtubules. While individual microtubules are dynamic, the
 microtubule array has been regarded as stationary. Using live-cell imaging
 of neurons in culture or in brain slices, combined with photoconversion
 techniques and pharmacological manipulations, we uncovered that the
 microtubule array flows retrogradely within neurites to the soma. This
 flow drives cycles of microtubule density, a hallmark of the fluctuating
 state before axon formation, thereby inhibiting neurite growth. The motor
 protein dynein fuels this process. Shortly after axon formation,
 microtubule retrograde flow slows down in the axon, reducing microtubule
 density cycles and enabling axon extension. Thus, keeping neurites short
 is an active process. Microtubule retrograde flow is a novel type of
 cytoskeletal dynamics, which changes the hitherto axon-centric view of
 neuronal polarization.
description: All data was obtained from live-cell imaging experiments that
 were performed on an Andor spinning disk Nikon Eclipse Ti microscope with
 Perfect Focus system (Nikon) and a Yokogawa CSU-X1 Spinning Disk Unit
 (CSUX1-A1N-E/FB2 5000rpm Control, FW, DMB 95L100016). Detailed methods for
 each experiment are available in the method section of the linked
 publication (upon acceptance; currently in revision).<br>
description: All scripts were written using
 Python 3.7 or 3.8, with environments build with conda (Anaconda Inc.;
 2020. Available from: https://docs.anaconda.com/) and using the following packages: SciPy 1.6.2 (for FigureFlow) or 1.5.2 (https://pypi.org/project/scipy/) (67), sci-kit image 0.17.2 or 0.18.1 (https://pypi.org/project/scikit-image/;) (68), numpy 1.20.3 (https://pypi.org/project/numpy/) (69), seaborn 0.11.1 (for FigureFlow) or 0.11.0  (https://pypi.org/project/seaborn/) (70), scikit-posthocs 0.6.7 (https://pypi.org/project/scikit-posthocs/) (71), matplotlib 3.34 or 3.4.2 (https://pypi.org/project/matplotlib/) (72), pandas 1.3.0 (for FigureFlow) or 1.1.3 (https://pandas.pydata.org/) (73), and python-pptx 0.6.19 (https://pypi.org/project/python-pptx/). For viewing data and for some manual analysis detailed in the methods section of the publication (upon acceptance; currently in revision) ImageJ (NIH, RRID: SCR_002074; https://imagej.nih.gov/ij/) was used, including several ImageJ plugins detailed in the methods section of the publication.