cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qrfj6q5hr
title: Tropical forest restoration in the Eastern Himalaya: Evaluating early survival and growth of native tree species

description: Asian tropical forests have among the highest rates of forest loss in the
 world. Ecological restoration is a vital step for biodiversity maintenance
 and climate change mitigation. For restoration practice, evaluation of
 species performance at early stages is crucial to avoid failure of the
 efforts and for screening species suitable to a region. Though the
 long-term performance of restoration plantings has been well-documented,
 few studies have evaluated the performance during the establishment of the
 planted saplings, especially in South and Southeast Asia. Restoration
 efforts in Northeast India, a region experiencing high forest loss, is
 limited by the lack of species-specific data on survival and growth. We
 compared inter-specific variation in seasonal survival and growth rates
 (diameter and height) for multiple native rainforest species from this
 region. We planted 3022 saplings of 50 species at a degraded open forest
 site. After 18 months, sapling survival varied between 9.1–94.3% for 32
 species, and only six species showed “excellent” survival after 18 months.
 Eight out of 17 species that were tested for seasonal variation in
 survival showed significant differences in survival between seasons. While
 the diameter growth rate varied for species between seasons, the height
 growth rate was different between both species and season, but the
 interaction term between species and season was not significant. Certain
 animal-dispersed, medium to large-seeded primary forest species performed
 well and are vital for future restoration efforts in this region.
description: Data of a study evaluating early survival and growth of native
 tree species, as part of the tropical forest restoration efforts in
 Arunachal Pradesh, Eastern Himalaya, India A study was
 carried out to evaluate the early performance in terms of survival and
 growth (stem diameter and height) of native tree species planted at a
 restoration site in a protected area site. The impact of seasons (wet and
 dry) on the performance of the tree species was also investigated in this
 study. The associated data of the study is uploaded here.
 Borawake_etal_EcologicalRestoration_Data.zip
DOI: 10.5061/dryad.02v6wwq4x
title: Antipredator responses of embryos and larval fathead minnows

description: Most research on embryonic learning and behavior in aquatic vertebrates
 has focused on fitness benefits after hatching, but the ability of embryos
 to perceive and respond to environmental stimuli may also have immediate
 adaptive value. Here, we examined whether fathead minnow embryos,
 Pimephales promelas, detect and respond to cues indicative of predation
 risk, and whether the embryonic environment influences behavior after
 hatching. We compared the behavior of 5-day post-fertilization (dpf)
 embryos reared in the presence or absence of olfactory alarm cue, alone or
 in combination with cues of a piscivorous predator (Bluegill sunfish,
 Lepomis macrochirus). Next, we reared larvae from the embryonic treatments
 to 21 dpf and tested them in two antipredator behavioral assays reflecting
 differences in the degree of immediate risk (predator avoidance vs attack
 evasion). Embryos that developed under perceived high-risk conditions
 exhibited reduced activity compared to those from low-risk environments.
 Larvae from high-risk environments also showed enhanced antipredator
 behavior, and evidence for embryonic predator learning. These data provide
 new insight into the learning capabilities and antipredator behaviors of
 aquatic vertebrate embryos.
description: Data for embryo activity and larval swimming behavior were
 automatically extracted from trial videos using behavioral tracking
 software (Ethovision XT and DanioScope, Noldus). Larval escape response
 data were manually measured from the trial videos by one researcher
 (CC).
DOI: 10.5061/dryad.ttdz08m0w
title: Dataset: DNA barcodes and microsatellites: how they complement for species identification in the complex genus Tamarix (Tamaricaceae)

description: DNA barcoding allows the identification of an organism by comparing the
 sequence of selected DNA regions (barcodes) with a previously compiled
 database, and it can be useful for taxonomic identification of species in
 complex genera, such as Tamarix. Many species of this genus show
 convergent morphology, which leads to frequent errors in their
 identification. Highly variable genetic markers, such as microsatellites
 or short sequence repeats (SSR), could be used to differentiate species
 where DNA barcodes fail. Here, we tested the ability of both, five
 different marker regions (rbcL, matK, ITS, trnH-psbA, and ycf1), and 14
 microsatellites, to properly identify Tamarix species, especially those
 from the Mediterranean Basin, and compared the pros and cons of the
 different analytical methods for species identification. DNA barcoding
 allows the genetic identification of certain species in Tamarix. The
 two-locus barcodes matK+ITS and ITS+ycf1 were the best-performing
 combinations, allowing up to 69% and 70%, respectively, correct
 identification. However, DNA barcoding failed in phylogenetically close
 groups, such as many Mediterranean species. The use of SSR can aid the
 identification of species, and the combination of both types of data (DNA
 barcoding and SSR) improved the success. The combination of data was
 especially relevant in detecting the presence of hybridization processes,
 which are common in the genus. However, caution must be exercised when
 choosing the clustering methods for the SSR data, since different methods
 can lead to very different results.
DOI: 10.5061/dryad.crjdfn35t
title: Edge disturbance shapes liana diversity and abundance but not liana-tree interaction network patterns in moist semi-deciduous forests, Ghana

description: Edge disturbance can drive liana community changes and alter liana-tree
 interaction networks, with ramifications for forest functioning.
 Understanding edge effects on liana community structure and liana-tree
 interactions is therefore essential for forest management and
 conservation. We evaluated the response of liana community structure and
 the patterns of liana-tree interaction structure to forest edge in two
 moist semi-deciduous forests in Ghana (Asenanyo and Suhuma Forest
 Reserves: AFR and SFR, respectively). Liana community structure and
 liana-tree interactions were assessed in 24 50 × 50 m randomly located
 plots in three forest sites in each forest: edge, interior and
 deep-interior established at 0-50 m, 200 m and 400 m from edge. Edge
 effects positively and negatively influenced liana diversity in forest
 edges of AFR and SFR, respectively. There was a positive influence of edge
 disturbance on liana abundance in both forests. We observed anti-nested
 structure in all the liana-tree networks in AFR, while no nestedness was
 observed in the networks in SFR. The networks in both forests were less
 connected, and thus more modular and specialised than their null models.
 Many liana and tree species were specialised, with specialisation tending
 to be symmetrical. The plant species played different roles in relation to
 modularity. Most of the species acted as peripherals (specialists), with
 only a few species having structural importance to the networks. The
 latter species group consisted of connectors (generalists) and hubs
 (highly connected generalists). Some of the species showed consistency in
 their roles across the sites, while the roles of other species changed.
 Generally, liana species co-occurred randomly on tree species in all the
 forest sites, except edge site in AFR where lianas showed positive
 co-occurrence. Our findings deepen our understanding of the response of
 liana communities and liana-tree interactions to forest edge disturbance,
 which are useful for managing forest edge.
DOI: 10.5061/dryad.gf1vhhmrh
title: Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red‐eared slider turtle

description: Non-native (invasive) species offer a unique opportunity to study the
 geographic distribution and range limits of species, wherein the
 evolutionary change driven by interspecific interactions between native
 and non-native closely related species is a key component. The red-eared
 slider turtle, Trachemys scripta elegans (TSE), has been introduced and
 successfully established worldwide. It can coexist with its native
 congeners T. cataspila, T. venusta and T. taylori in Mexico. We performed
 comprehensive fieldwork, executed a battery of genetic analyses and
 applied a novel species distribution modeling approach to evaluate their
 historical lineage relationships and contemporary population genetic
 patterns. Our findings support the historical common ancestry between
 native TSE and non-native (TSEalien), while also highlighting the genetic
 differentiation of the exotic lineage. Genetic patterns are associated
 with their range size/endemism gradient, the microendemic T. taylori
 showed significant reduced genetic diversity and high differentiation,
 whereas TSEalien showed the highest diversity and signals of population
 size expansion. Counter to our expectations, lower naturally occurring
 distribution overlap and little admixture patterns were found between TSE
 and its congeners, exhibiting reduced gene flow and clear genetic
 separation across neighboring species despite having zones of contact. We
 demonstrate that these native Trachemys species have distinct climatic
 niche suitability, likely preventing establishment of and displacement by
 the TSEalien. Moreover, we found major niche overlap between TSEalien and
 native species worldwide, supporting our prediction that sites with closer
 ecological optima to the invasive species have higher establishment risk
 than those that are closer to the niche-center of the native species.
description: The dataset includes 261 samples, comprising individuals from the
 field, traded turtles of unknown origin, and museum samples, including: 69
 turtle individuals of <i>Trachemys venusta</i>, 13 <i>T.
 cataspila</i>, 12 <i>T. taylori</i>, 128 non-native
 <i>Trachemys scripta elegans
 </i>TSE<sub>alien</sub> and 39 native TSE (see Table S1
 from the Supporting Information provided with the Mol Ecol
 Publication). We amplified 15 polymorphic
 microsatellite loci for 256 individuals (genepop file), and
 obtained GBS data for a final dataset after filtering
 including 160 samples (vcf file).
description: The final GBS data file has an average number of loci/sample =
 55,982, coverage = 16x, and 63,385 SNPs.
DOI: 10.5061/dryad.7pvmcvdvd
title: Data from: Corticosteroid-binding globulin deficiency independently predicts mortality in septic shock

description: Context Hydrocortisone administration in septic shock remains
 controversial. Corticosteroid-binding globulin (CBG) transports cortisol
 to inflammatory sites and is depleted in septic shock. Objective To
 determine if severely deficient serum CBG &lt;200 nmol/L (Ref range
 269-641 nmol/L) independently predicts septic shock mortality. Methods A
 prospective observational study in patients with septic shock. Patients
 were categorised into two groups: mean plasma CBG concentrations
 &lt;200 nmol/L and ≥200 nmol/L (day 1/2), with additional
 categorisation by nadir CBG. Primary outcome was ICU mortality. Secondary
 outcomes were 28- and 90-day mortality, norepinephrine requirements,
 renal-replacement therapy, and clinician-instituted hydrocortisone.
 Results 135 patients were included. Mortality rates in ICU were higher in
 the CBG &lt;200 nmol/L vs the CBG ≥200 nmol/L group: 32.4% vs 13.9%;
 Odds ratio (OR), 2.97, (95% confidence intervals (CI) 1.19,7.41); P=0.02:
 28-days; OR 2.25 (95% CI 0.99,5.11): 90-days; OR 2.21 (95% CI 0.99,4.91).
 Multivariate analysis revealed 4 factors independently associated with ICU
 mortality: CBG &lt;200 nmol/L (OR 3.23, 95% CI 1.06,9.88), Acute
 Physiology and Chronic Health Evaluation II &gt;25 (OR 3.58, 95% CI
 1.20,10.68); SOFA liver score (OR 1.98, 95% CI 1.04,3.72); and
 renal-replacement therapy (OR 6.59, 95% CI 2.17,20.01). Nadir CBG levels
 were associated with higher SOFA cardiovascular scores, norepinephrine
 total dose (ug) P&lt;0.01 and duration (days) P&lt;0.01. Plasma
 cortisol concentrations and hydrocortisone administration did not relate
 to ICU mortality. Conclusion Septic shock patients with CBG &lt;200
 nmol/L had higher norepinephrine requirements and 3.2-fold higher ICU
 mortality. CBG concentration was the only directly reversible independent
 mortality risk factor.
DOI: 10.5061/dryad.3xsj3txhz
title: Data from: Geographic variation of litter chemistry and palatability in an invasive plant versus its native competitor

description: Aim: Latitudinal variation in biotic interactions is recognized as a
 driver underlying variation in plant invasion success and therefore an
 important issue in conservation biogeography. However, previous studies
 have mainly focused on interactions between living plants and herbivores,
 whereas litter traits and detritivory have been hardly studied along
 latitude or compared between native and invasive plants. Our aim was to
 compare latitudinal variation in leaf-litter chemistry and palatability to
 detritivores between invasive and native plants, and investigate which
 chemical traits determine detritivory and whether they are climate-driven.
 Location: China. Taxa: Spartina alterniflora, Phragmites australis,
 Porcellio laevis, Chiromantes dehaani. Methods: We combined field surveys
 with laboratory experiments to compare latitudinal variation in litter
 chemistry between the widespread invasive Spartina alterniflora and its
 native competitor Phragmites australis across their co-occurring range
 (20.9–40.7°N, ~2200km). For both species, we examined litter palatability
 to two common detritivores (Porcellio laevis and Chiromantes dehaani)
 along the same latitude. We also analyzed relationships among climate,
 litter traits, and detritivory. Results: In five out of nine litter
 traits, we found latitudinal clines, with little difference between the
 two plant species in how they responded across the gradient. Litter
 palatability decreased with increasing latitude, but was generally higher
 in Spartina than Phragmites. Two key litter traits (C:P ratio and
 flavonoid content) were significantly associated with temperature of
 origin and with detritivory. Main conclusions: There were geographic
 clines in litter traits and palatability, with strong links between
 climate, litter chemistry and detritivory, in both Spartina and
 Phragmites. Spartina litter, however, was more rapidly decomposed by
 detritivores, which could create positive feedbacks, and contribute to the
 successful Spartina invasion along China’s coast. Future ecological
 restoration projects should therefore dispose Spartina plant tissue or
 litter off-site, to reduce the competitiveness of Spartina and support the
 conservation of native Phragmites.
description: Please see
 <strong>README</strong>.docx for
 details.
DOI: 10.15468/dl.v7c34u
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Jania ungulata",
 "Year 1902-2013"
 ]
}

 The dataset includes 53 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003033-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4mw6m90c3
title: A roadmap to reconstructing muscle architecture from CT data

description: Skeletal muscle is responsible for voluntary force generation across
 animals, and muscle architecture largely determines the parameters of
 mechanical output. The ability to analyze muscle performance through
 muscle architecture is thus a key step towards better understanding the
 ecology and evolution of movements and morphologies. In pennate skeletal
 muscle, volume, fiber lengths and attachment angles to force transmitting
 structures comprise the most relevant parameters of muscle architecture.
 Measuring these features through tomographic techniques offers an
 alternative to tedious and destructive dissections, particularly as the
 availability of tomographic data is rapidly increasing.  However,
 there is a need for streamlined computational methods to access this
 information efficiently. Here, we establish and compare workflows using
 partially automated image analysis for fast and accurate estimation of
 animal muscle architecture. After isolating a target muscle through
 segmentation, we evaluate freely available and proprietary fiber tracing
 algorithms to reconstruct muscle fibers. We then present a script using
 the Blender Python API to estimate attachment angles, fiber lengths,
 muscle volume and Physiological Cross-Sectional Area. We apply these
 methods to insect and vertebrate muscle and provide guided workflows.
 Results from fiber tracing are consistent compared to manual measurements
 but much less time-consuming. Lastly, we emphasize the capabilities of the
 open-source 3D software Blender as both a tool for visualization and a
 scriptable analytic tool to process digitized anatomical data. Across
 organisms, it is feasible to extract, analyze, and visualize muscle
 architecture from tomography data by exploiting the spatial features of
 scans and the geometric properties of muscle fibers. As digital libraries
 of anatomies continue to grow, the workflows and approach presented here
 can be part of the open-source future of digital comparative
 analysis. 
description: Please refer to the ReadMe on what individual files are and what
 they're for. Data is structured into full ant
 dataset, resampled ant dataset, bird dataset in separate .zip
 folders
DOI: 10.5061/dryad.dv41ns20n
title: Effects of future climate change on the forests of Madagascar

description: Global climate change is continuing to occur at an alarming rate. In
 addition to increases in global weather extremes, melting of polar ice
 caps and subsequent sea level-rises, climate change is known to directly
 impact the life-cycles and ecologies of many animals and plants. Whilst
 climate change is projected to result in substantial geographic range and
 habitat contractions for many species in the future, the effects of
 climate change on many habitats of conservation-concern remain poorly
 understood. In this study, we investigated how future climate change is
 projected to impact the occurrence and distribution of four major forest
 types of Madagascar, a global biodiversity hotspot and conservation
 priority, over the next 60 years. We also compared how climate change
 effects vary among the four forest types under a “mitigation” climate
 forecast, and under a “business-as-usual” trajectory. As expected, our
 models suggest that future climate change will affect the distribution of
 the four forest types under both trajectories, and forest occurrence is
 likely to decrease if mean temperatures, temperature seasonality, and
 precipitation rates increase as predicted. The exception being that forest
 gain is predicted to occur in the north-west of Madagascar, resulting in a
 small increase in transitional forest area under the “business-as-usual”
 climate change trajectory. Our study highlights that unmitigated climate
 change will have a negative impact on Madagascar’s forests during the
 period up to the year 2080, and climate change therefore needs to be
 mitigated. Madagascar remains a global conservation priority, and urgent
 conservation action and protective legislation is required to safeguard
 the future of its native forest.
description: This dataset contains 1) a zip file containing all raster layers
 for the current and future time scenarios, and under both climate
 trajectories, 2) a zip file of bias files for each of the four forest
 types, and 3) thinned occurence point datasets (CSV) for each of the four
 forest types.
DOI: 10.5061/dryad.vhhmgqnvw
title: Ecuadorian Plant-Hummingbird interactions over an elevation gradient in the Andes, sampled with camera traps in 11 localities

description: Community ecologists have made great advances in understanding how natural
 communities can be both diverse and stable by studying communities as
 interaction networks. However, focus has been on interaction networks
 aggregated over time, neglecting the consequences of the seasonal
 organization of interactions, henceforth seasonal structure, for community
 stability. Here, we extended previous theoretical findings on the topic in
 two ways: (i) by integrating empirical seasonal structure of 11
 plant-hummingbird communities into dynamic models, and (ii) by tackling
 multiple facets of network stability together. We show that, in a
 competition context, seasonal structure enhances community stability by
 allowing diverse and resilient communities while preserving their
 robustness to species extinctions. The positive effects of empirical
 seasonal structure on network stability vanished when using randomized
 seasonal structures, suggesting that eco-evolutionary dynamics produce
 stabilizing seasonal structures. We also show that the effects of seasonal
 structure on community stability are mainly mediated by changes in network
 structure and productivity, suggesting that the seasonal structure of a
 community is an important and yet neglected aspect in the
 diversity-stability and diversity-productivity debates.
description: We used data from 11 independent sites in the tropical forests of
 Ecuador (Table 1, Fig. S1) in which interactions among flowering plants
 and hummingbirds were recorded along transects by using camera traps, as
 described in Graham & Weinstein (2018). Graham
 CH, Weinstein BG. Towards a predictive model of species interaction beta
 diversity. Ecol Lett. 2018;21(9):1299–310.
DOI: 10.5061/dryad.qz612jmh5
title: IFNγ-primed periodontal ligament cells regulate T cell responses via IFNγ-inducible mediators and ICAM-1-mediated direct cell contact

description: Periodontal ligament
 (PDL) cells help maintain tissue
 homeostasis by balancing tissue inflammation and
 regeneration. However, the mechanisms by
 which interferon γ (IFNγ) modulates this process are not yet fully understood.The present study aimed to examine the effect of primed and unprimed PDL cells with IFNγ on the viability and differentiation of T lymphocytes and its functional consequences. The results showed that IFNγ-primed PDL cells possessed enhanced immunosuppression by suppressing T lymphocyte viability and directing T lymphocyte differentiation towards a higher Th2/Th1 ratio. Suppression of T cell viability was mainly mediated by IFNγ-inducible secreted mediators, which was prevented in the presence of direct cell contact, likely by intercellular adhesion molecule-1 (ICAM-1)-induced PI3K-mediated TGFβ1 expression in PDL cells. In contrast, ICAM-1 activation augmented IFNγ-induced IFNγ and IL-6 expression in PDL cells, which in turn modulated T cell differentiation. The resulting interaction between these two cell types activated macrophage and suppressed osteoclast differentiation. In conclusion, the results have shown, for the first time, that primed and unprimed PDL cells with IFNγ differentially control T cell responses via IFNγ-inducible mediators and ICAM-1-mediated direct cell contact, suggesting the role of PDL cells in shifting an inflammatory phase towards a regenerative phase.