cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8cz8w9gpg
title: Data from : Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China

description: Aim: There have been numerous studies of forest-soil microbial
 biogeography, but an integrated view of edaphic factors, plant, climatic
 factors, and geographic distance in determining the variation of bacterial
 community and assembly processes remains unclear at large spatial scales.
 Here, we analyzed the factors affecting the biogeographic pattern and
 assembly processes of soil bacterial communities under 58 tree species in
 five natural mountain forests. Location: Eastern China. Major taxa
 studied: Bacterial communities. Methods: Hierarchical partitioning
 analysis and distance decay models were performed to evaluate the relative
 contributions of plant phylogeny, environmental, and spatial variables to
 the composition of bacterial communities. We applied the Nearest Taxon
 Index (NTI), β-Nearest Taxon Index (βNTI), and the modified Raup-Crick
 metric to reveal the mechanisms of bacterial assembly processes. Results:
 We found that plant phylogeny accounted for a significant, but minor,
 fraction (0.7%) of the variation in composition of bacterial communities.
 In contrast, soil pH was the primary determinant of bacterial diversity
 and community composition, independently explaining 68.6% and 69.9% of the
 variation, respectively. Based on the NTI analysis, bacterial community
 assembly was more phylogenetically clustered with increasing soil pH.
 Variable selection was the predominant process explaining bacterial
 community assembly when differences in soil pH were ≥ 0.83, whereas
 homogenizing dispersal dominated when differences in soil pH were &lt;
 0.83. However, there was no significant relationship between plant
 phylogenetic distance and βNTI. Main conclusions: Our findings provide
 strong evidence that soil pH predominantly determines bacterial
 distribution and mediates the relative impact of stochasticity and
 determinism in soil bacterial community assembly. This suggests that
 climate-change associated forest soil acidification could have a dramatic
 impact on soil bacterial diversity, composition, and function.
description: The files contain the
 phylogenetic trees of plant and bacteria. The .mts file can be opened with
 MEGA6
DOI: 10.5061/dryad.3n5tb2rgc
title: Data for: Contrasting response of native and non-native plants to disturbance and herbivory in mountain environments

description: Aim: Climate warming and increasing human disturbance are expected to
 promote non-native plant invasions in mountain ecosystems. Although
 biological invasions are also expected to be modulated by biotic
 interactions, it is still not clear how invertebrate herbivores can affect
 plant invasion dynamics. Using a large manipulative experiment, we aimed
 at testing: 1) the effect of soil disturbance and elevation on native and
 non-native plant communities, and 2) the effect of plant-herbivore
 interactions, nitrogen deposition, and elevation in driving plant
 establishment after soil disturbance. Location: European Alps, NE Italy
 Taxon: Vascular plants Methods: We selected remote, uninvaded dry
 semi-natural grasslands along the core elevational range of non-native
 plants in the European Alps (0-1330 m) and manipulated soil disturbance,
 nitrogen deposition, and invertebrate herbivory. Then, we followed the
 natural establishment under real field conditions of both native and
 non-native plants over one growing season. We used generalized
 mixed-effects models to test the effects of the experimental treatments.
 Results: Native and non-native species showed contrasting responses to
 soil disturbance and elevation. Low elevations and disturbance promoted
 non-native success, while affecting native species diversity negatively.
 Two-thirds of the experimental sites acquired novel non-natives after
 disturbance. Most of the observed non-natives were not present in the
 surrounding vegetation as mature plants, indicating that propagules were
 able to reach even remote natural areas. While current N deposition levels
 did not affect plant establishment, we found that after disturbance
 invertebrate herbivory might play an important role in facilitating
 non-native invasions by reducing native cover. Main conclusions: Our
 findings show that highly resistant ecosystems such as continuous
 grasslands can be easily invaded once the resident vegetation has been
 removed, and that natural herbivory pressure from invertebrates might
 amplify the negative effects of disturbance on resident native species
 irrespective of elevation. Together, these results indicate increasing
 risks of future plant invasions on mountains under global change.
DOI: 10.5061/dryad.pk0p2ngmt
title: Short-Tandem-Repeat (STR) marker set for Eurasian lynx for article: Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland

description: Conservation and management of large carnivores requires knowledge of
 female and male dispersal. Such information is crucial to evaluate the
 population’s status and thus management actions. This knowledge is
 challenging to obtain, often incomplete and contradictory at times. The
 size of the target population and the methods applied can bias the
 results. Also, population history and biological or environmental
 influences can affect dispersal on different scales within a study area.
 We have genotyped Eurasian lynx (180 males and 102 females, collected
 2003-2017) continuously distributed in southern Finland (~23,000 km2)
 using 21 short tandem repeats (STR) loci and compared statistical genetic
 tests to infer local and sex-specific dispersal patterns within and across
 genetic clusters as well as geographic regions. We tested for sex-specific
 substructure with individual-based Bayesian assignment tests and spatial
 autocorrelation analyses. Differences between the sexes in genetic
 differentiation, relatedness, inbreeding, and diversity were analysed
 using population-based AMOVA, F-statistics, and assignment indices. Our
 results showed two different genetic clusters that were spatially
 structured for females but admixed for males. Similarly, spatial
 autocorrelation and relatedness was significantly higher in females than
 males. However, we found weaker sex-specific patterns for the Eurasian
 lynx when the data were separated in three geographical regions than when
 divided in the two genetic clusters. Overall, our results suggest
 male-biased dispersal and female philopatry for the Eurasian lynx in
 Southern Finland. The female genetic structuring increased from west to
 east within our study area. In addition, detection of male-biased
 dispersal was dependent on analytical methods utilized, on whether subtle
 underlying genetic structuring was considered or not, and the choice of
 population delineation. Conclusively, we suggest using multiple genetic
 approaches to study sex-biased dispersal in a continuously distributed
 species in which population delineation is difficult.
description: This data set is the result of an ongoing collaboration between
 the Natural Resources Institute Finland (Luke) and the Norwegian Institute
 of Bioeconomy Research (NIBIO).  For details on sample
 collection, laboratory methods, and statistical analyses, please see the
 article: Genetic analysis indicates spatial-dependent patterns of
 sex-biased dispersal in Eurasian lynx in Finland.
DOI: 10.5061/dryad.9w0vt4bdt
title: Deletion of the sodium/hydrogen exchanger 6 causes low bone volume in adult mice

description: The sodium/hydrogen exchanger 6 (NHE6) localizes to recycling endosomes,
 where it mediates endosomal alkalinization through K+/H+ exchange.
 Mutations in the SLC9A6 gene encoding NHE6 cause severe X-linked mental
 retardation, epilepsy, autism and corticobasal degeneration in humans.
 Patients with SLC9A6 mutations exhibit skeletal malformations, and a
 previous study suggested a key role of NHE6 in osteoblast-mediated
 mineralization. The goal of this study was to explore the role of NHE6 in
 bone homeostasis. To this end, we studied the bone phenotype of NHE6
 knock-out mice by microcomputed tomography, quantitative histomorphometry
 and complementary ex vivo and in vitro studies. We detected NHE6
 transcript and protein in both differentiated osteoclasts and mineralizing
 osteoblasts. In vitro studies with osteoclasts and osteoblasts derived
 from NHE6 knock-out mice demonstrated normal osteoclast differentiation
 and osteoblast proliferation without an impairment in mineralization
 capacity. Microcomputed tomography and bone histomorphometry studies
 showed a significantly reduced bone volume and trabecular number as well
 as an increased trabecular space at lumbar vertebrae of 6 months old NHE6
 knock-out mice. The bone degradation marker c-terminal telopeptides of
 type I collagen was unaltered in NHE6 knock-out mice. However, we observed
 a reduction of the bone formation marker procollagen type 1 N-terminal
 propeptide, and increased circulating sclerostin levels in NHE6 knock-out
 mice. Subsequent studies revealed a significant upregulation of sclerostin
 transcript expression in both primary calvarial cultures and femora
 derived from NHE6 knock-out mice. Thus, loss of NHE6 in mice causes an
 increase of sclerostin expression associated with reduced bone formation
 and low bone volume.
description: See detailed information in published manuscript
 (https://pubmed.ncbi.nlm.nih.gov/34508879/) and attached README
 file.
description: See detailed information in attached README file.
DOI: 10.5061/dryad.nvx0k6drh
title: Dispersal propensity and distance in relation to sex and body mass of roe deer

description: Evolution should favour plasticity in dispersal decisions in response to
 spatial heterogeneity in social and environmental context. Sex differences
 in individual optimisation of dispersal decisions are poorly documented in
 mammals, because species where both sexes disperse are rare. To elucidate
 the sex-specific drivers governing dispersal, we investigated sex
 differences in condition-dependence in the propensity and distance of
 natal dispersal in one such species, the roe deer, using fine-scale
 monitoring of 146 GPS-collared juveniles in an intensively monitored
 population in south-west France. Dispersal propensity increased with body
 mass in males such that 36% of light individuals dispersed, whereas 62% of
 heavy individuals did so, but there was no evidence for
 condition-dependence in dispersal propensity among females. In contrast,
 dispersal distance increased with body mass at a similar rate in both
 sexes such that heavy dispersers travelled around twice as far as light
 dispersers. Sex differences in the strength of condition-dependent
 dispersal may result from different selection pressures acting on
 behaviour of males and females. We suggest that females disperse prior to
 carrying capacity being reached, likely in relation to the risk of
 inbreeding. In contrast, natal dispersal in males is likely governed by
 competitive exclusion through male-male competition for breeding
 opportunities in this strongly territorial mammal. Our study is, to our
 knowledge, a first demonstration that condition-dependence in dispersal
 propensity and dispersal distance may be decoupled, indicating contrasting
 selection pressures drive the behavioural decisions of whether or not to
 leave the natal range, and where to settle.
description: See Methods of Hewison et al. 
description: Data are in "data_dispersal" Codes
 for analysis are in "script" Explanation of
 codes in data file are in
 "data_dispersal_codes_readme"
DOI: 10.5061/dryad.qbzkh18gj
title: Large oaks Quercus robur have increased at Tumhem's oak meadow

description: We have described a significant increase in the number of large oaks
 Quercus robur in the Tunhem oak meadow during 23 years. We define
 large oak as having a circumference at chest height larger than 250
 centimeters. The number of large oaks have increased by 29 percent from
 our first survey in 1996 to our second survey in 2019. Most of the
 recruitment of larger oaks are in the smaller size-classes from 250 to 400
 centimeters. Nineteen oaks have died during our study
 period.  We have found that very large oaks have a similar
 continuous growth as smaller large oaks. They have increased in
 circumference from 0.5 to 4.5 centimeters. Oaks standing in open areas
 increase more in circumference (34.8 cm) compared to half-shaded (32.1 cm)
 and shaded large oaks (28.3 cm). 
description: Data on the number of large oaks Quercus robur in the Tunhem oak
 meadow collected in 1996 and in 2019. Circumference at chest height was
 measured.
DOI: 10.5061/dryad.wh70rxwmq
title: Keystone species affect the relationship between soil microbial diversity and ecosystem function under land use change in subtropical China

description: Soil microbial diversity affects soil chemical cycling and ecosystem
 function. However, how highly connected keystone species regulate
 associated microbial structure and function (of the whole community and of
 specialized species), irrespective of their abundance under land use
 change, remains unresolved. Here, we identified the relationship between
 microbial diversity [soil phospholipid fatty acid (PLFA) richness and
 composition, and ammonia-oxidizing archaea and bacteria (AOA and AOB)
 communities] with both a broad (i.e., microbial respiration) and
 specialized function (i.e., nitrification rate) in a woodland, shrubland,
 and adjacent cropland in subtropical China. Microbial respiration was
 significantly positively related to the microbial richness, but negatively
 correlated with the keystone species richness across different land use
 types. The relationships between biodiversity and the broad ecosystem
 function varied with land use, with a stronger relationship in the
 afforested land compared with in the cropland. In contrast to the broad
 function, land use did not significantly affect the specialized function,
 but the specialized function was positively related to AOA richness in the
 cropland. Additionally, the specialized function was predominately driven
 by the keystone species composition in AOA and AOB communities and
 indirectly regulated by soil environmental factors (particularly soil
 temperature) across land uses. Overall, our results provide direct
 experimental insight into the mechanisms underlying the role of the
 keystone species in regulating belowground ecosystem functions under land
 use change. In particular, our findings reveal that the broad function is
 maintained by the niche compensation effect, while the specialized
 function is maintained by the identity effect.
DOI: 10.15468/dl.45x6et
title: Occurrence Download

description: A dataset containing 354 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Daviesia acicularis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 354 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002768-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pc866t1nc
title: Asymmetric evolvability leads to specialization without trade-offs

description: Many organisms are specialized, and these narrow niches are often
 explained with trade-offs—inability for one organism to express maximal
 performance in two or more environments. However, evidence is lacking that
 trade-offs are sufficient to explain specialists. Several lines of
 theoretical inquiry suggest that populations can specialize without
 explicit trade-offs, as a result of relaxed selection in generalists for
 their performance in rare environments. Here I synthesize and extend these
 approaches, showing that emergent asymmetries in evolvability can push a
 population toward specialization in the absence of trade-offs and in the
 presence of substantial ecological costs of specialism. Simulations are
 used to demonstrate how adaptation to a more common environment interferes
 with adaptation to a less common but otherwise equal alternative
 environment, and that this interference is greatly exacerbated at low
 recombination rates. This adaptive process of specialization can
 effectively trap populations in a suboptimal niche. These modeling results
 predict that transient differences in evolvability across traits during a
 single episode of adaptation could have long-term consequences for a
 population’s niche.
description: All data analyzed in the paper result from simulations. Both the
 code for producing these results and analyzing them are
 included. 
description: Please see the included readme file for instructions.
DOI: 10.5061/dryad.z612jm6bg
title: Data from: Evidence of economical territory selection in a cooperative carnivore

description: As an outcome of natural selection, animals are likely adapted to select
 territories economically by maximizing benefits and minimizing costs of
 territory ownership. Theory and empirical precedent indicate that a
 primary benefit of many territories is exclusive access to food resources,
 and primary costs of defending and using space are associated with
 competition, travel, and mortality risk. A recently-developed mechanistic
 model for economical territory selection provided numerous empirically
 testable predictions. We tested these predictions using location data from
 gray wolves (Canis lupus) in Montana, USA. The dataset included here
 contains the territory size estimates for each collared wolf and the
 characteristics of territories.
description: These values are specific to the time and place collected (see
 details in the manuscript).
DOI: 10.5061/dryad.x95x69phb
title: Growth-defense tradeoffs shape the genetic composition of aspen forests

description: All organisms experience fundamental conflicts between divergent metabolic
 processes. In plants, a pivotal conflict occurs between allocation to
 growth, which accelerates resource acquisition, and to defense, which
 protects existing tissue against herbivory. Tradeoffs between growth and
 defense traits are not universally observed, and a fundamental prediction
 of plant evolutionary ecology is that context-dependence of these
 tradeoffs contributes to the maintenance of intraspecific variation in
 defense. This prediction has rarely been tested, however, and the
 evolutionary consequences of growth-defense tradeoffs in different
 environments are poorly understood. Here we show that intraspecific trait
 tradeoffs interact with competitive environment to drive natural selection
 of tree genotypes corresponding to their growth-defense phenotypes. Our
 results show for the first time that a functional trait tradeoff, when
 coupled with environmental variation, causes real-time divergence in the
 genetic architecture of forest stands. Specifically, competitive selection
 for faster growth resulted in dominance by fast-growing tree genotypes
 that were poorly defended against natural enemies. This outcome is a
 signature example of eco-evolutionary dynamics: competitive interactions
 affected microevolutionary trajectories on a timescale relevant to
 subsequent ecological interactions. Eco-evolutionary drivers of tree
 growth and defense are thus critical to stand-level trait variation, which
 structures communities and ecosystems over expansive spatiotemporal
 scales.
DOI: 10.17909/n6mq-s211
title: JWST ERS NIRISS/SOSS data of WASP-18b

description: This data is part of ERS-1366 from the JWST Transiting Exoplanet Community observations of the ultra-hot Jupiter WASP-18b with the NIRISS/SOSS.
DOI: 10.5061/dryad.fxpnvx0r1
title: Chemical defense strategies, induction timing, growth, and tradeoffs in Pinus aristata and Pinus flexilis

description: Tradeoffs among plant defense investment and fitness traits, including
 growth, are often invoked to explain evolutionary strategies targeted at
 resisting herbivores. Many Pinus species have specialized herbivores,
 including the mountain pine beetle, Dendroctonus ponderosae, (MPB), and
 have historically been a focus of defense investigations. We compared
 defense traits of two high-elevation Pinus species, P. aristata and P.
 flexilis, that are hosts to MPB and hypothesized to have different growth
 and defense traits and potential tradeoffs. Interspecific differences were
 assessed by sampling trees within the same stands, and intraspecific
 differences were assessed by sampling stands at sites across latitudes
 where both species co-occurred. Constitutive defenses were measured at day
 0, and the timing, concentration, and composition of an induced resin
 defense response was assessed by sampling at 1, 4, and 30 days following
 either mechanical wounding only or a simulated MPB attack using its
 primary fungal symbiont Grosmannia clavigera. At day 4, induced resin
 concentrations did not differ between mechanical wounding and simulated
 MPB attack in either species. By day 30, resin defense concentrations in
 response to simulated MPB attack were greater than response to mechanical
 wounding and were &gt;19-fold greater than constitutive levels.
 Results suggest that initial induced resin defense responses in the two
 species are likely generalized, with a delayed response that is targeted
 specifically at MPB and G. clavigera. At all sites, P. aristata had higher
 concentrations of constitutive and day 30 induced resin defenses compared
 to P. flexilis, although P. flexilis induced proportionately more.
 Tradeoffs in growth and defense between the species were only found at the
 two most climatically favorable sites where P. aristata grew slower than
 P. flexilis. No tradeoffs were found between the two defense types at
 either biological scale. Overall, our findings highlight that the two pine
 species growing in the same stands 1) have a delayed response to a
 specialized native herbivore and fungal symbiont, 2) only exhibited
 interspecific defense-growth tradeoffs at two climatically favorable
 sites, and showed no intraspecific defense-growth tradeoffs, 3) showed no
 tradeoffs between constitutive and induced defenses at either biological
 scale, and 4) have evolved different defense strategies.
description: see Methods; Soderberg et al. 2022
DOI: 10.5061/dryad.rv15dv47g
title: Food webs for three burn severities after wildfire in the Eldorado National Forest, California

description: We provide data on ecological community responses to wildfire, collected
 three years post-fire, across three burn conditions (unburned, moderate
 severity and high severity) in the Eldorado National Forest, California.
 The data were collected with 19 sampling methods deployed across 27 sites
 (nine in each burn condition) used to estimate richness, body size,
 abundance and biomass density for 849 species (including 107 primary
 producers, 634 invertebrates, 94 vertebrates). The sampling methods are
 detailed in a companion data paper. To maximize transparency and ease of
 use we have made our data available in four formats: Raw, tidy, temporary
 and summary. Raw data is as close as possible to the form in which it was
 collected. As such, raw data is not ready for analysis. We have provided
 tidy versions of each raw data set that are ready for analysis. Temporary
 data files are included for transparency but are used to create summary
 data files, and not intended to be informative as stand alone products.
 Summary data files provide estimated biomass densities and network
 structure for each of our three burn categories. All tidy and summary data
 files are accompanied by metadata files describing their contents. We
 provide the R code to transform raw data files into tidy, temporary and
 summary files. We have included the code necessary to reproduce our work.
 We have broken the code into three R scripts: Biomass density estimation,
 resource filters assignment and network assembly.
description: The methods used to collect the data are described in an
 companion data paper. The methods used to tidy and summarize the data are
 in the included R scripts.