cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02v6wwq18
title: Inferred genetic architecture underlying evolution in a fossil stickleback lineage

description: Inferring the genetic architecture of evolution in the fossil record is
 difficult because genetic crosses are impossible, the acquisition of DNA
 is usually impossible, and phenotype-genotype maps are rarely obvious.
 However, such inference is valuable because it reveals the genetic basis
 of microevolutionary change across many more generations than is possible
 in studies of extant taxa, thereby integrating microevolutionary process
 and macroevolutionary pattern. Here, we infer the genetic basis of pelvic
 skeleton reduction in Gasterosteus doryssus, a Miocene stickleback fish
 from a finely resolved stratigraphic sequence that spans nearly 17,000
 years. Reduction in pelvic score, a categorical measure of pelvic
 structure, resulted primarily from reciprocal frequency changes of two
 discrete phenotypic classes. Pelvic vestiges also showed left-side-larger
 asymmetry. These patterns implicate Pitx1, a large-effect gene whose
 deletion generates left-larger asymmetry of pelvic vestiges in extant,
 closely-related Gasterosteus aculeatus. In contrast, reductions in lengths
 of the pelvic girdle and pelvic spines resulted from directional shifts of
 unimodal, continuous trait distributions, suggesting an additional suite
 of genes with minor, additive pelvic effects, again like G. aculeatus.
 Similar genetic architectures explain shared but phyletically independent
 patterns across 10 million years of stickleback evolution.
description: Please see the manuscript for details.
description: <strong>Phenotypic.data.for.analysis.no.sc.csv</strong> Univariate traits measured for fossil specimens from 18 sections of temporal sequence K. Missing data are due to taphonomic reasons or because traits have been lost, and are indicated by NAs. Trait abbreviations are described in KSeries_abbreviations.doc. <strong>Sample_L_Pelvic_Frequencies_fromTravis_May2019.csv</strong> This table is equivalent to Supplementary Table S2. It is a frequency table of pelvic score by section. <strong>univariate.data.L.fromTableS4_forAnalysis.csv</strong> This is the temporal sequence L data set used for pelvic asymmetry analysis. In the R code, we've noted that times reported in YEAR (col D) and INT (col E) are miscalibrated. This is okay, however, as chronology is not necessary for the asymmetry analyses, except to make sure that only lineage II fish are analyzed. The arrival of lineage II can be correlated with Supplementary Table S2 by finding where mean PS goes from ~1 to exactly 3.0 for several thousand years. This happens at INT = 5250 years, which means that fish from earlier in the sequence are lineage I and were excluded for the analyses. <strong>Dryad_StuartTravisBell.R</strong> This R script should recreate the results and figures in the paper. You will have to set your working directory define the path to the data files. Otherwise, it should run cleanly. If there are errors, or if results insconsistent with the manuscript appear, please write to Yoel Stuart (ystuart@luc.edu).
DOI: 10.5061/dryad.hqbzkh1d2
title: Nitrate removal and N2O production from upflow and downflow column woodchip bioreactors

description: Woodchip denitrifying bioreactors (WDBR) reduce off-field tile drainage
 nitrogen (N) losses from agricultural fields.  Limited evaluation
 exists regarding the influence of flow direction through WDBRs. 
 Changing flow direction could reduce short circuiting.  This
 study evaluated the dependency of nitrate-nitrogen removal and dissolved
 nitrous oxide (dN2O) production rates on vertical flow direction in
 triplicate column bioreactors at 12-h (without carbon dosing) and 2-h
 (with carbon dosing) hydraulic residence times.  Results
 presented demonstrate that there was no significant difference in overall
 nitrogen removal rates from these column bioreactors as a function of flow
 direction.  There was the suggestion of lower nitrous oxide (N2O)
 production in the downflow direction, although this was not statistically
 significant due to the high variability of the N2O production observed in
 the upflow direction.  Carbon addition led to bioclogging of
 downflow columns; future work needs to identify dosing rate, placement,
 and conditions that prevent biofilm formation.
description: This
 dataset is supplement to: Feyereisen, G.W., K.A. Spokas, J.S. Strock, D.J. Mulla, A.Z. Ranaivoson, and J.A. Coulter. 2020. Nitrate removal and N<sub>2</sub>O production from upflow and downflow column woodchip bioreactors. Agric. Environ. Lett. The Materials and Methods in this paper describe how the data were obtained and analyzed.
description: The data download includes a Read_me.pdf file that explains the
 data files, defines the column headings, and identifies the variable
 units.
DOI: 10.15468/dl.xz9qv9
title: Occurrence Download

description: A dataset containing 2170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bituminaria bituminosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2170 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002443-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pc866t1kz
title: Species diversity and food web structure jointly shape natural biological control in agricultural landscapes

description: Land-use change and agricultural intensification concurrently impact
 natural enemy (e.g., parasitoid) communities and their associated
 ecosystem services (ESs), i.e., biological pest control. However, the
 extent to which (on-farm) parasitoid diversity and food webs mediate
 landscape-level influences on biological control remains poorly
 understood. Here, drawing upon a 3-year study of quantitative
 parasitoid-hyperparasitoid trophic networks from 25 different
 agro-landscapes, we assess the cascading effects of landscape composition,
 species diversity and trophic network structure on ecosystem functionality
 (i.e., parasitism, hyperparasitism). Path analysis further reveals
 causality leading to the biological control of a resident crop pest, i.e.,
 Aphis gossypii. Functionality is dictated by (hyper)parasitoid diversity,
 with its effects modulated by food web generality and vulnerability.
 Non-crop habitat cover directly benefits biological control, whereas
 secondary crop cover indirectly lowers hyperparasitism. Our work
 underscores a need to simultaneously account for on-farm biodiversity and
 trophic interactions when investigating ESs within dynamic
 agro-landscapes.
description: The study contained a
 3-year study of quantitative parasitoid-hyperparasitoid trophic networks
 from 25 different agro-landscapes along with a gradient of crop and
 non-crop habitats. We assess the cascading effects of landscape
 composition, species diversity and trophic networks structure on ecosystem
 functionality (i.e., parasitism, hyperparasitism). General linear model
 (GLM) analysis with multiple model selection inference were first
 performed to assess the direct effects of explanatory variables belonging
 to the same groups (such as landscape composition, species diversity,
 quantitative food web metrics) on each response variable. Linear mixed
 effect model (LMM) analysis then helped assess the direct effects of
 combinational predictors belonging to three groups: landscape composition,
 species richness and diversity, and food web features, on ESs and EDSs.
 Path analysis with structural equation models (SEMs) further reveals
 causality leading to the biological control of a resident crop pest, i.e.,
 Aphis gossypii. Functionality is dictated by (hyper)parasitoid diversity,
 with its effects modulated by two key metrics of food web generality and
 vulnerability. Non-crop habitat cover directly benefits biological
 control, whereas secondary crop cover indirectly lowers
 hyperparasitism.
description: We analyzed a dataset
 of 3-year parasitoid-hyperparasitoid trophic networks from 25 different
 agro-landscapes. Using path analysis, we uncover how species diversity and
 food web structure shape ecosystem functionality. Locaiton: the northern
 China
DOI: 10.5061/dryad.sf7m0cg3r
title: Phylogenetic and ecomorphologic diversifications of spiriferinid brachiopods after the end-Permian extinction

description: The Order Spiriferinida spanning the latest Ordovician to Early Jurassic
 is a small group of brachiopods overshadowed by other taxa-rich clades
 during the Paleozoic. It diversified significantly after the end-Permian
 extinction and became one of the four major clades of Triassic
 brachiopods. However, the phylogeny and recovery dynamics of this clade
 during the Triassic still remain unknown. Here, we present a higher-level
 parsimony-based phylogenetic analysis of Mesozoic spiriferinids to reveal
 their evolutionary relationships. Ecologically related characters are
 analyzed to indicate the variances in ecomorphospace occupation and
 disparity of spiriferinids through the Permian-Triassic transition. For
 comparison with potential competitors of the spiriferinids, the
 pre-extinction spiriferids are also included in the analysis. Phylogenetic
 trees demonstrate that about half of the Mesozoic families appeared during
 the Anisian, indicating the greatest phylogenetic diversification
 at that time. Triassic spiriferinids re-occupied a large part of
 the ecomorphospace released by its competitor spiriferids during the
 end-Permian extinction; they also fully exploited the cyrtiniform region
 and developed novel lifestyles. Ecomorphologic disparity of the
 spiriferinids dropped greatly in the Early Triassic, but it rebounded
 rapidly and reached the level attained by the pre-extinction spiriferids
 in the Late Triassic. The replacement in ecomorphospace occupation between
 spiriferids and spiriferinids during the P-Tr transition clearly indicates
 that the empty ecomorphospace released by the extinction of Permian
 spiriferids was one of the important drivers for the diversification of
 the Triassic spiriferinids. The Spiriferinida took over the empty
 ecomorphospace and had the opportunity to flourish.
DOI: 10.5061/dryad.v15dv41tf
title: Clinician-researcher’s perspectives on clinical research during the COVID-19 pandemic

description: Objectives: The outcome of well-performed clinical research is essential
 for evidence-based patient management during pandemics. However,
 conducting clinical research amidst a pandemic requires researchers to
 balance clinical and research demands. We seek to understand the values,
 experiences, and beliefs of physicians working at the onset of the
 COVID-19 pandemic in order to inform clinical research planning. We aim to
 understand whether pandemic settings affect physician comfort with
 research practices, and how physician experiences shape their
 understanding of research in a pandemic setting. Methods: A survey tool
 was adapted to evaluate familiarity and comfort with research during a
 pandemic. A cross-sectional, online questionnaire was distributed across
 Canadian research networks early in the COVID-19 outbreak. The survey was
 administered between March 11th and 17th, 2020, during a time of local
 transmission but prior to the surge of cases. We aimed to recruit into the
 survey physicians in infectious disease and critical care research
 networks across Canada. Results: Of the 133 physician respondents, 131
 (98%) considered it important to conduct clinical research during the
 COVID-19 pandemic. Respondents were more accepting of adaptations to the
 research process during a pandemic compared to in a non-pandemic setting,
 including conducting research with deferred consent (χ2 = 8.941, 95% CI:
 -0.264, -0.085, p = 0.003), using non-identifiable observational data with
 a waiver of consent with a median score of 97 out of 100 (IQR: 79.25–100)
 vs median 87 out of 100 (IQR: 63–79) (95% CI: -12.43, 0.054, p = 0.052).
 The majority felt that research quality is not compromised during
 pandemics. Conclusions: Physicians consider it important to conduct
 research during a pandemic, highlighting the need to expedite research
 activities in pandemic settings. Respondents were more accepting of
 adaptations to the research process for research conducted during a
 pandemic, compared to that conducted in its absence of a pandemic.
DOI: 10.5061/dryad.5x69p8d12
title: Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)

description: The use of high-throughput sequencing technologies to produce genome-scale
 datasets was expected to settle some long-standing controversies across
 the Tree of Life, particularly in areas where short branches occur at deep
 timescales. Instead, these datasets have often yielded many well-supported
 but conflicting topologies, and highly variable gene-tree distributions. A
 variety of branch-support metrics beyond the nonparametric bootstrap are
 now available to assess how robust a phylogenetic hypothesis may be, as
 well as new methods to quantify gene-tree discordance. We applied ten
 branch support metrics to an ancient group of marine fishes (Teleostei:
 Pelagiaria) whose interfamilial relationships have proven difficult to
 resolve due to a rapid accumulation of lineages very early in its history.
 We analyzed hundreds of loci including published
 ultraconserved and newly generated exonic data along with their
 flanking regions to represent all 16 extant families for more than 150 out
 of 284 valid species in the group. Branch support was typically lower at
 inter- than intra-familial relationships regardless of the type
 of marker. Several nodes that were highly supported with bootstrap had
 very low site and gene-tree concordance, revealing underlying conflict.
 Combining exons with their flanking regions increased branch lengths in
 the deep branches of the pelagiarian tree. Despite this conflict, we were
 able to identify four consistent interfamilial clades,
 each comprised of two or three families. Our results
 demonstrate the limitations of employing current metrics of branch support
 and species-tree estimation when assessing the confidence of ancient
 evolutionary radiations and emphasize the necessity to embrace alternative
 measurements to explore phylogenetic uncertainty and discordance in
 phylogenomic datasets.
description: <b>These files include:</b> <b>Supplementary Figures:</b> Figures S1 to S9 <b>Supplementary Tables:</b> Tables S1 to S2 in SI_Pelagiaria.docx <b>Other Supplementary Materials:</b> Appendix 1: Dataset 1 – Exons (344 taxa & 1,104 markers) Appendix 2: Dataset 2 – Exons + flanks (293 taxa & 1,104 markers) Appendix 3: Dataset 3 – Exons (313 taxa & 1,087 markers) Appendix 4: Dataset 4 – Exons + flanks (281taxa & 1,087 markers) Appendix 5: Dataset 5 – Exons (204 taxa & 1,087 markers) Appendix 6: Dataset 6 – Exons + flanks (204 taxa & 1,087 markers) Appendix 7: List of alternative topologies tested in PhyParts and Quartet Sampling results for each subset Appendix 8: Summary of the exon dataset properties on a per locus basis Appendix 9: Summary of the exons + flanks dataset properties on a per locus basis
DOI: 10.5061/dryad.h70rxwdgd
title: Fixed or mixed? variation in tree functional types and vegetation structure in a forest-savanna ecotone in West Africa

description: We analysed thirty-five 400-m2 plots encompassing forest, savanna and
 intermediate vegetation types in an ecotonal area in Ghana, West Africa.
 Across all plots, fire frequency was over a period of 15 years relatively
 uniform (once in 2–4 years). Although woodlands were dominated by species
 typically associated with savanna-type formations, and with forest
 formations dominated by species usually associated with closed canopies,
 these associations were non-obligatory and with a discrete non-specialized
 species grouping also identified. Across all plots, crown area index, stem
 basal area and above-ground biomass were positively associated with higher
 soil exchangeable potassium and silt contents: this supporting recent
 suggestions of interplays between potassium and soil water storage
 potential as a significant influence on tropical vegetation structure. We
 also found an average NDVI cover increase of ~0.15% year−1 (1984–2011)
 with plots dominated by non-specialized species increasing more than those
 dominated by either forest- or savanna-affiliated species. Our results
 challenge the traditional view of a simple forest vs. savanna dichotomy
 controlled by fire, and with our newly identified third non-specialized
 species grouping also potentially important in understanding ecotonal
 responses to climate change.
description: Refer to the uploaded file
DOI: 10.5061/dryad.9w0vt4bcf
title: Data from: Where Am I? Niche constraints due to morphological specialisation in two Tanganyikan cichlid fish species

description: Food resource specialisation within novel environments is considered a
 common axis of diversification in adaptive radiations. Feeding
 specialisations are often coupled with striking morphological adaptations
 and exemplify the relation between morphology and diet
 (phenotype-environment correlations), as seen in, for example, Darwin
 finches, Hawaiian spiders and, in particular, the cichlid radiations in
 East Africa. The cichlids’ potential to rapidly exploit and occupy a
 variety of different habitats has previously been attributed to the
 variability and adaptability of their trophic structures including the
 pharyngeal jaw apparatus. Here we report a reciprocal transplant
 experiment designed to explore the adaptability of the cichlid’s trophic
 structures in highly specialised cichlid fish species. More specifically,
 we forced two common but ecologically distinct cichlid species from Lake
 Tanganyika, Tropheus moorii (rock-dweller) and Xenotilapia boulengeri
 (sand-dweller), to live on their preferred as well as on an un-preferred
 habitat (sand and rock, respectively). We measured their overall
 performance on the different habitat types and explored whether adaptive
 phenotypic plasticity is involved in adaptation. We found that, while
 habitat had no effect on the performance of X. boulengeri, T. moorii
 performed significantly better in its preferred habitat. Despite an
 experimental duration of several months we did not find a shift in the
 morphology of the lower pharyngeal jaw bone that would be indicative of
 adaptive phenotypic plasticity in this trait.
DOI: 10.5061/dryad.f4qrfj6tf
title: Climate change exposure and vulnerability of the global protected area estate from an international perspective

description: Aim: Protected areas are essential to conserve biodiversity and ecosystem
 benefits to society under increasing human pressures of the Anthropocene.
 Anthropogenic climate change, however, threatens the enduring
 effectiveness of protected areas in conserving biodiversity and providing
 ecosystem services, because it modifies and redistributes biodiversity
 with unknown consequences for ecosystem functioning within protected
 areas. Here we assess (1) the climate change exposure of the global
 terrestrial protected area estate and (2) the climate change vulnerability
 of national protected area estates. Location: Terrestrial protected areas
 worldwide. Methods: We calculated local climate change exposure as
 predicted climate anomalies between the present and 2070 using ten global
 climate models, two emission scenarios (RCP 4.5 and 8.5) and the finest
 spatial resolution available for global climate projections (approx. 1
 km). We estimated the climate change vulnerability of national protected
 area estates by analysing countrywide relationships between protected
 areas’ climate anomalies and other protected area characteristics, i.e.
 area, elevation, terrain ruggedness, human footprint and irreplaceability
 for globally threatened species. Results: We found predicted climate
 anomalies highest in protected areas of (sub-)tropical countries. The
 correlations between climate anomalies and protected area characteristics
 strongly differ between countries. Globally, protected areas showing large
 climate anomalies tend to be at high elevation and highly irreplaceable
 for threatened species, increasing climate change vulnerability. These
 protected areas are relatively large in area, of high topographic
 heterogeneity and less pressured by humans, decreasing climate change
 vulnerability. Main conclusion: This study reveals potential hotspots of
 climate change impact inside the terrestrial protected area estate. It
 thus supports and guides climate-smart conservation policy and management,
 particularly national to local authorities, to ensure the future
 effectiveness of protected areas in preserving biodiversity and ecosystem
 benefits under climate change.
description: This dataset is a product of the corresponding paper. Please see
 the Methods section for further information.
DOI: 10.5061/dryad.q573n5tgc
title: Data from: Symbiotic soil fungi enhance resistance and resilience of an experimental grassland to drought and nitrogen deposition

description: Ecosystem stability is threatened by multiple global change factors such
 as drought and elevated nitrogen deposition. Yet, it is still poorly
 understood whether soil organisms can buffer against such perturbations.
 Here we focus on arbuscular mycorrhizal fungi (AMF), a common and
 widespread group of soil fungi. AMF form symbiotic associations with the
 majority of terrestrial land plants and promote a range of ecosystem
 services including plant production, diversity and nutrient cycling. We
 tested whether AMF have the ability to enhance the resistance and
 resilience of plant communities under soil moisture deficit (hereby
 drought) and nitrogen deposition. Grassland microcosms with 11 different
 plant species were established with and without AMF and exposed to
 elevated nitrogen levels and to an intermittent period of drought. Drought
 strongly reduced plant productivity and nitrogen cycling, but had limited
 effects on plant diversity. Nitrogen enrichment reduced plant diversity
 and increased nitrogen leaching and N2O emissions. The presence of AMF
 enhanced plant productivity, plant diversity, and reduced nitrogen losses.
 AMF facilitated the resistance of plant productivity and nitrogen cycling
 to drought and the recovery of the plant community structure back to its
 pre drought state. Furthermore, AMF also mitigated the adverse effects of
 nitrogen enrichment on the resistance of multiple ecosystem functions to
 drought. Synthesis. Our work highlights the integral role of AMF for the
 stability of ecosystem functioning; AMF are not only able to promote
 resistance to harsh conditions of global change, but also improve
 resilience by enabling plant communities to recover. These findings
 underline AMF’s insurance capacity to buffer ecosystems against global
 change.
description: Our experiment was set up as
 a complete randomized block and fully crossed design with three factors:
 ‘drought’ (W, normal/drought), ‘N deposition’ (N, low/high), and ‘AMF’
 (with/without AMF). And our experiment included three periods, e.g.
 "predrought", "drought", "recovery", each
 period included 11 weeks. At the end of each period, we harvested biomass,
 tested N<sub>2</sub>O emission, simulated rainfall and
 collected leachate.