cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m0s2k02
title: Data from: Mismatches between breeding phenology and resource abundance of resident alpine ptarmigan negatively affect chick survival

description: 1. Phenological mismatches – defined here as the difference in
 reproductive timing of an individual relative to the availability of its
 food resources – occur in many avian species. Mistiming breeding
 activities in environments with constrained breeding windows may have
 severe fitness costs due to reduced opportunities for repeated breeding
 attempts. Therefore, species occurring in alpine environments may be
 particularly vulnerable. 2. We studied fitness consequences of timing of
 breeding in an alpine-endemic species, the white-tailed ptarmigan (Lagopus
 leucura), to investigate its influence on chick survival. We estimated
 phenological mismatch by measuring plant and arthropods used by ptarmigan
 in relation to their timing of breeding. 3. We monitored 120 nests and 67
 broods over a three-year period (2013–2015) at three alpine study sites in
 the Rocky Mountains of Colorado. During this same period we actively
 monitored food resource abundance in brood-use areas to develop year and
 site specific resource phenology curves. We developed several mismatch
 indices from these curves that were then fit as covariates in
 mark-recapture chick survival models. 4. A correlation analysis between
 seasonal changes in arthropod and food plant abundance indicated that a
 normalized difference vegetation index (NDVI) was likely the best
 predictor for food available to hens and chicks. A survival model that
 included an interaction between NDVI mismatch and chick age received
 strong support and indicated young chicks were more susceptible to
 mismatch than older chicks. 5. We provide evidence that individual females
 of a resident alpine species can be negatively affected by phenological
 mismatch. Our study focused on individual females and did not examine if
 phenological mismatch was present at the population level. Future work in
 animal populations occurring in mountain systems focusing on a combination
 of both individual- and population-level metrics of mismatch will be
 beneficial.
description: MARK chick survival
 modelsZipped file contains two
 files: 1) a MARK DBF file, and 2) a MARK FTP file. Both are required to
 open and view MARK chick survival models. To view, unzip files into the
 same folder. Requires Program MARK (www.phidot.org) to
 open.wtpt_chick_survival_dryad.zip
DOI: 10.5061/dryad.97vq77g
title: Data from: Migratory shorebird adheres to Bergmann’s Rule by responding to environmental conditions through the annual lifecycle

description: The inverse relationship between body size and environmental temperature
 is a widespread ecogeographic pattern. However, the underlying forces that
 produce this pattern are unclear in many taxa. Expectations are
 particularly unclear for migratory species, as individuals may escape
 environmental extremes and reorient themselves along the environmental
 gradient. In addition, some aspects of body size are largely fixed while
 others are environmentally flexible and may vary seasonally. Here, we used
 a long‐term dataset that tracked multiple populations of the migratory
 piping plover Charadrius melodus across their breeding and non‐breeding
 ranges to investigate ecogeographic patterns of phenotypically flexible
 (body mass) and fixed (wing length) size traits in relation to latitude
 (Bergmann's Rule), environmental temperature (heat conservation
 hypothesis), and migratory distance. We found that body mass was
 correlated with both latitude and temperature across the breeding and
 non‐breeding ranges, which is consistent with predictions of
 Bergmann's Rule and heat conservation. However, wing length was
 correlated with latitude and temperature only on the breeding range. This
 discrepancy resulted from low migratory connectivity across seasons and
 the tendency for individuals with longer wings to migrate farther than
 those with shorter wings. Ultimately, these results suggest that wing
 length may be driven more by conditions experienced during the breeding
 season or trade‐offs related to migration, whereas body mass is modified
 by environmental conditions experienced throughout the annual lifecycle.
description: plover_bergmannR data file containing the data required to determine geographic patterns in piping plover body size as a function of latitude or seasonal temperature.
DOI: 10.5061/dryad.t32st70
title: Data from: Evaluating the influences of temperature, primary production, and evolutionary history on bivalve growth rates

description: Organismal metabolic rates reflect the interaction of environmental and
 physiological factors. Thus, calcifying organisms that record growth
 history can provide insight into both their own physiology and life
 history and the ancient environments in which they lived. However,
 interpreting them requires understanding which environmental factors have
 the greatest influence on growth rate, and to what extent evolutionary
 history constrains growth rates across lineages. We integrated satellite
 measurements of sea surface temperature and chlorophyll-a concentration
 with a database of growth coefficients, body sizes, and lifespans for 692
 populations of living marine bivalves in 195 species, set within the
 context of a new maximum likelihood phylogeny of bivalves. We find that
 environmental predictors overall explain only a small proportion of
 variation in growth coefficient across all species; temperature is a
 better predictor of growth coefficient than food supply, and growth
 coefficient is somewhat more variable at higher summer temperature. Growth
 coefficients exhibit moderate phylogenetic signal and taxonomic membership
 is a stronger predictor of growth coefficient than any environmental
 predictor, but phylogenetic inertia cannot fully explain the disjunction
 between our findings and the extensive body of work demonstrating strong
 environmental control on growth rates within taxa. Accounting for
 evolutionary history is critical when considering shells as historical
 archives. The weak relationship between variation in food supply and
 variation in growth coefficient in our dataset is inconsistent with the
 hypothesis that the increase in mean body size through the Phanerozoic was
 driven by increasing productivity enabling faster growth rates.
description: Bivalve feeding
 ecologySpecies-level
 assignments of bivalve feeding ecology. Sources included in the
 .csv.Saulsbury et al 2019 R
 codeR
 code used for all analyses in the paper.Saulsbury et al 2019
 Supplementary DataSupplementary data
 referred to in the analysis. Includes 5 sections: "Phylogenetic
 methods," "Supplementary Data 2: Growth coefficients and the
 test of phylogenetic signal," "Choice of predictors,"
 "Joint tests of equality of slopes," and "Phylogeny and
 effect sizes."Saulsbury_et_al_2019_accession_numbersGenbank accession numbers corresponding to molecular data used in inferring bivalve phylogeny.Saulsbury_et_al_2019_alignmentNexus file containing the molecular sequence alignment used in phylogenetic inference.Saulsbury_et_al_2019_order-level_constraint_treeA constraint tree used in phylogenetic inference, based on previous phylogenetic studies of Bivalvia (see Supplementary Data 1).Saulsbury_et_al_2019_partition_filePartition file used as input for RAxML. One partition for each of four genes.Saulsbury_et_al_2019_SequenceMatrix_outputAlignment metadata generated by SequenceMatrix.Saulsbury_et_al_2019_tree_fileMolecular phylogeny used in downstream analyses.
DOI: 10.5061/dryad.6n7v8r3
title: Data from: Gradual evolution towards flightlessness in Steamer-Ducks

description: Flightlessness in birds is the product of changes in suites of
 characters--including increased body size and reduced anterior limbs--that
 have evolved repeatedly and independently under similar ecological
 conditions (generally insularity). It remains unknown whether this
 phenotypic convergence extends to the genomic level, partially because
 many losses of flight occurred long ago (such as in penguins or ratites),
 thus complicating the study of the genetic pathways to flightlessness.
 Here we use genome sequencing to study the evolution of flightlessness in
 a group of ducks that are current and dynamic exemplars of this major
 functional transition. These recently diverged Tachyeres steamer-ducks
 differ in their ability to fly: one species is predominantly flighted and
 three are mainly flightless. Through a genome-wide association analysis we
 identify two narrow candidate genomic regions implicated in the
 morphological changes that led to flightlessness, and reconstruct the
 number of times flightnesses has evolved in Tachyeres. The strongest
 association is with DYRK1A, a gene that when knocked-out in mice leads to
 alterations in growth and bone morphogenesis. These findings, together
 with phylogenetic and demographic analyses, imply that the genomic changes
 leading to flightlessness in Tachyeres may have evolved once, and that
 this trait remains functionally polymorphic in two species.
description: Unfiltered SNP
 datasetThis file contains the
 output from the GATK GenotypeGVCFs module that has not undergone
 filtering. The samples are identified by sequencing library, but can be
 matched back to specimen using the README.txt file.UNFILTERESD_SNP_SET_TACHYERES.vcf.gzFiltered SNP datasetThis file contains the filtered set of SNPs used in the study. It was derived from the UNFILTERESD_SNP_SET_TACHYERES.vcf.gz file and individuals are identified in the same way as in that file.second_filter_LOW_MISSING_TACHYERES.vcf.gzAligned mitochondrial genomes56_mtgenomes.nexFiles for GPhoCS analysisThese files are the input and control (.ctl) files used to conduct the GPhoCS analysiscombined_nomaf_1k.fastaFiles for Structure analysis (all species together)This file was used to generate the Structure plot in Figures 2 and S330miss_thin_50kb.str
DOI: 10.5061/dryad.gn52t27
title: Data from: Using plant functional distances to select species for restoration of mining sites

description: 1. Plant facilitation, an ecological interaction that benefits at least
 one species without harming the other, is increasingly used as a
 restoration tool. To restore degraded habitats under a facilitation
 framework, practitioners must correctly select both the benefactor (nurse)
 and the beneficiary (facilitated) species. 2. Based on community assembly
 and species coexistence theory, we propose selecting plant species that
 largely differ in a suite of functional traits so that competition is
 minimized and facilitation maximized due to functional complementarity. To
 apply this guideline in a pilot restoration experiment performed in
 metalliferous mine tailings in South-Eastern Spain, we first built the
 plant-plant facilitative interaction network naturally occurring in a set
 of 12 tailings. After characterizing each species with 20 morphological
 and physiological traits, we verified that facilitative interactions were
 predominantly established between functionally distant species. 3. Then,
 we designed a sowing experiment combining 50 nurse-facilitated species
 pairs separated by a wide range of functional distances. The success of
 seedling establishment significantly increased with the functional
 distance between the nurse and the facilitated plant species. 4. Synthesis
 and applications. We encourage to use ecological facilitation together
 with trait-based species selection to design restoration programmes based
 on the principle of increasing functional distance between target species.
 This method may not only promote the restoration of the plant cover but
 also impact paramount ecosystem functions, thus being an efficient low
 cost restoration practice in abiotically stressful ecosystems.
description: Navarro-Cano_et_al2019_dryadSheet &lt;&gt;: Data of seedling emergence of 10 sowed species beneath 5 different nurse plants in a metal mine tailing in SE Spain.Sheet &lt;&gt;: Functional distance between pairs of nurse-sowed species.Navarro-Cano_et_al2019a_dryadFacilitated plant species and their abundances in patches and adjacent gaps in metal mine tailings from SE Spain
DOI: 10.5061/dryad.2f70818
title: Data from: Differences in carbon stocks along an elevational gradient in tropical mountain forests of Colombia

description: Tropical mountain forests provide an exceptional opportunity to evaluate
 the patterns of variation of carbon stocks along elevational gradients
 that correspond to well-defined temperature gradients. We predicted that
 carbon stored in live aboveground biomass, aboveground necromass, and soil
 components of forests on the eastern flank of the Colombian Andes would
 change with elevation along this gradient extending from 750 to 2800 m
 above sea level. The rationale was that the corresponding change in
 temperature (14°C to 26°C) would influence tree growth and decomposition
 of organic matter. To address this hypothesis, we examined the carbon
 stored in these three components using data from 20 0.25-ha plots located
 along this elevational gradient. The mean total carbon stock found in the
 study region was 241.3±37.5 Mg C/ha. Aboveground carbon stocks decreased
 with elevation (p =0.001), as did necromass carbon stocks (p =0.016).
 Although soil organic carbon stocks did not differ significantly along the
 gradient (p =0.153), they contributed proportionately more at higher than
 at lower elevations, counterbalancing the opposite trends in aboveground
 carbon and necromass carbon stocks. As such, total carbon stocks did not
 vary significantly along the elevational gradient (p =0.576).
description: Carbon Components in
 Mountain Forests in Colombia20 permanent plots of
 0.25-ha (50 m x 50 m) were established along the elevational gradient
 following Feeley et al. (2011) (Table S1; Fig. S1). The plots were
 distributed across ten elevational sections, each with a range of 250 m
 asl. The average horizontal distance between plots was 6.48 km (median:
 5.72 km; range: 0.29-17.4 km). Within each plot, we measured, mapped and
 tagged all trees and palms ≥10 cm diameter at breast height (DBH)
 following standardized methods for long-term tropical forest dynamics
 plots (Condit 1998). In the case of tree species with buttresses, diameter
 was measured 50 cm above them. In all cases, the DBH point was painted and
 measured with diameter tape calibrated to one millimeter. We excluded
 arborescent ferns and lianas. Total height (H, in m) was measured on 40
 percent of the individuals within each plot, using either a telescopic
 Hastings fiberglass rod (H &lt;15 m) or a Nikon laser 550 electronic
 hypsometer (H ≥15 m).DATA.txt
DOI: 10.5061/dryad.df19750
title: Data from: Piceatannol attenuates RANKL-induced osteoclast differentiation and bone resorption and promotes caspase3-mediated apoptosis of mature osteoclasts

description: Osteoclasts are multinuclear giant cells that have unique ability to
 degrade bone. The search for new medicines that modulate the formation and
 function of osteoclasts is a potential approach for treating
 osteoclast-related bone diseases. Piceatannol (PIC), a natural organic
 polyphenolic stilbene compound found in diverse plants with a strong
 antioxidant and anti-inflammatory effect. However, the effect of PIC on
 bone health has not been scrutinized systematically. In this study, we
 used RAW264.7, a osteoclast lineage cells of murine macrophages, to
 investigate the effects and the underlying mechanisms of PIC on
 osteoclasts . Here, we demonstrated that PIC treatment ranging from 0 to
 40μM strongly inhibited osteoclast formation and bone resorption in a
 dose-dependent manner. Furthermore, the inhibitory effect of PIC was
 accompanied by the decrease of osteoclast-specific genes. At the molecular
 level, PIC suppressed the phosphorylation of c-Jun N-terminal kinase
 (JNK), extracellular signal-regulated kinase (ERK1/2), NF-κB p65, IκBα and
 AKT. Besides, PIC promoted the apoptosis of mature osteoclasts by inducing
 caspase-3 expression. In conclusion, our results suggested that PIC
 inhibited RANKL-induced osteoclastogenesis and bone resorption by
 suppressing MAPK, NF-κB and AKT signaling pathways and promoted
 caspase3-mediated apoptosis of mature osteoclasts, which might contribute
 to the treatment of bone diseases characterized by excessive bone
 resorption.
description: supplemental
 Fig1The pre-experiments for
 cell viability assay of RAW264.7 cells.(A)48h; (B)72hsupplemental
 Fig2The negative control
 group of Figure 1D.Cell
 viabilityRaw data for
 CCK-8TRAP cell
 countRaw data for TRAP cell
 count.TRAP
 activityRaw data for TRAP
 activity assay.Real-time
 qPCRRAW data for Real-time
 qPCR. (Note: 结果 translated is result)
DOI: 10.5061/dryad.nh57s00
title: Data from: Chronic phosphorus enrichment and elevated pH suppresses Quercus spp. leaf litter decomposition in a temperate forest

description: The potential of excessive nitrogen (N) suppressing litter decay in is
 widely recognized. The role of phosphorus (P) in plant litter decay is
 less understood and is generally assumed to have a weak influence in
 decomposition outside tropical or wetland ecosystems. Based on the
 “microbial mining” hypothesis that suggests the availability of limiting
 nutrients is the driving mechanism of decay, P could have a strong
 influence on carbon (C) cycling in low-P ecosystems. The objective of this
 study was to determine if increasing P availability will influence the
 decomposition of leaf litter in a low-P temperate forested ecosystem. If
 the availability of a limiting nutrient is a driving mechanism mediating
 decay, then increasing the availability of P in a low-P environment should
 inhibit decay. The experiment was held in a low-P mixed mesophytic forest
 in the unglaciated Alleghany Plateau (USA). Since 2009, P availability has
 been increased either directly by phosphate fertilizer and/or indirectly
 by raising soil pH. Starting in 2011 and for three consecutive years,
 Quercus spp. leaf litter bags were deployed and harvested at least every
 year for three years for temporal replication. After three years,
 elevating pH and/or P litter mass loss was ~52% and significantly (P
 &lt; 0.001) lower than the control at 73% mass loss. The mean
 residence time (MRT; k yr-1) for the control was 2.1 years, but elevating
 P with pH increased MRT to 5.3 years. Results support the “microbial
 phosphorus mining” hypothesis that P has the potential to inhibit decay
 for Quercus spp. leaf litter in temperate forests and potentially increase
 soil C.
description: Soil, litter, and mass
 loss measurmentsContains raw data for
 soil mineral properties & processes (Table 1), Quercus spp. litter
 chemistry (Table 2), and from the litter bag experiment (Figures 2 &
 3).DeForest2019_SBB.xlsx
DOI: 10.5061/dryad.b537cs5
title: Data from: Species diversification and phylogenetically constrained symbiont switching generated high modularity in the lichen genus Peltigera

description: 1. Ecological interactions range from purely specialized to extremely
 generalized in nature. Recent research has showed very high levels of
 specialization in the cyanolichens involving Peltigera (mycobionts) and
 their Nostoc photosynthetic partners (cyanobionts). Yet, little is known
 about the mechanisms contributing to the establishment and maintenance of
 such high specialization levels. 2. Here, we characterized interactions
 between Peltigera and Nostoc partners at a global scale, using more than
 one thousand thalli. We used tools from network theory, community
 phylogenetics and biogeographical history reconstruction to evaluate how
 these symbiotic interactions may have evolved. 3. After splitting the
 interaction matrix into modules of preferentially interacting partners, we
 evaluated how module membership might have evolved along the mycobionts’
 phylogeny. We also teased apart the contributions of geographical overlap
 vs phylogeny in driving interaction establishment between Peltigera and
 Nostoc taxa. 4. Module affiliation rarely evolves through the splitting of
 large ancestral modules. Instead, new modules appear to emerge
 independently, which is often associated with a fungal speciation event.
 We also found strong phylogenetic signal in these interactions, which
 suggests that partner switching is constrained by conserved traits.
 Therefore, it seems that a high rate of fungal diversification following a
 switch to a new cyanobiont can lead to the formation of large modules,
 with cyanobionts associating with multiple closely retated Peltigera
 species. 5. Finally, when restricting our analyses to Peltigera sister
 species, the latter differed more through partner acquisition/loss than
 replacement (i.e., switching). This pattern vanishes as we look at sister
 species that have diverged longer ago. This suggests that fungal
 speciation may be accompanied by a stepwise process of (1) novel partner
 acquisition and (2) loss of the ancestral partner. This could explain the
 maintenance of high specialization levels in this symbiotic system where
 the transmission of the cyanobiont to the next generation is assumed to be
 predominantly horizontal. 6. Synthesis. Overall, our study suggests that
 oscillation between generalization and ancestral partner loss may maintain
 high specialization within the lichen genus Peltigera, and that partner
 selection is not only driven by partners’ geographical overlap, but also
 by their phylogenetically conserved traits.
description: Peltigera
 datasetDescription of sampled
 thalli for this studyPeltigera dryad
 dataset.txt
DOI: 10.5061/dryad.b30mh0p
title: Data from: Crop identity and memory effects on aboveground arthropods in a long-term crop rotation experiment

description: Agricultural landscapes are globally dominated by monocultures under
 intensive management. This is one of the main reasons for biodiversity
 loss and insect population decline in many regions all over the world.
 Agroecosystem biodiversity in these areas can be enhanced by cropping
 system diversification, such as crop rotations. Yet, long-term studies on
 effects of crop rotations on aboveground agrobiodiversity are lacking. We
 set up a 10-year long-term crop-rotation experiment in Central Germany and
 monitored the temporal dynamics of aboveground arthropods over a full
 cultivation period to investigate influence of current and preceding crop
 identity and cropping system diversification on activity density, species
 richness and community structure. We found that species composition was
 strongly influenced by currently grown crop although effect on arthropods
 varied between species groups. Especially winter oilseed rape strongly
 affects arthropod community structure. Interestingly, we were also able to
 show an influence of the preceding crops, indicating an ecological memory
 effect in aboveground arthropod community. Our results show that crop
 identity of both currently and previously grown crops in crop rotations
 may lead to an increase of arthropod activity density and changes in
 species composition. Diversified crop rotations including appropriate
 crops can be an easily implemented tool to increase arthropod biodiversity
 and biomass at large spatial and temporal scales, particularly in areas
 dominated by a single crop (e.g. wheat, maize). Our results may help to
 design optimized crop rotations for large-scale enhancement of insect
 biodiversity in agroecosystems.
description: Data_Meyer_et_al_-_Crop_identity_and_memory_effects_on_aboveground_arthropods_in_a_long-term_crop_rotation_experimentIn the dataset, we present data about the experimental design, management, soil mesofauna and aboveground species in a long-term crop rotation experiment.