cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1vhhmgqv6
title: Seed dormancy varies widely among Arabidopsis thaliana populations both between and within Fennoscandia and Italy

description: The timing of germination is a key life-history trait in plants, which is
 strongly affected by the strength of seed dormancy. Continental-wide
 genetic variation in seed dormancy has been related to differences in
 climate and the timing of conditions suitable for seedling establishment.
 However, for predictions of adaptive potential and consequences of
 climatic change, information is needed regarding the extent to which seed
 dormancy varies within climatic regions and the factors driving such
 variation. We quantified dormancy of seeds produced by 17 Italian and 28
 Fennoscandian populations of Arabidopsis thaliana when grown in the
 greenhouse and at two field sites in Italy and Sweden. To identify
 possible drivers of among-population variation in seed dormancy, we
 examined the relationship between seed dormancy and climate at the site of
 population origin, and between seed dormancy and flowering time. Seed
 dormancy was on average stronger in the Italian compared to the
 Fennoscandian populations, but also varied widely within both regions.
 Estimates of seed dormancy in the three maternal environments were
 positively correlated. Among Fennoscandian populations, seed dormancy
 tended to increase with increasing summer temperature and decreasing
 precipitation at the site of population origin. In the smaller sample of
 Italian populations, no significant association was detected between mean
 seed dormancy and climate at the site of origin. The correlation between
 population mean seed dormancy and flowering time was weak and not
 statistically significant within regions. The correlation between seed
 dormancy and climatic factors in Fennoscandia suggests that at least some
 of the among-population variation is adaptive and that climate change will
 affect selection on this trait. The weak correlation between population
 mean seed dormancy and flowering time indicates that the two traits can
 evolve independently.
description: See publication: Zacchello, G., S. Bomers, C. Böhme, F. M.
 Postma, and J. Ågren. Seed dormancy varies widely among
 <i>Arabidopsis thaliana</i> populations both between and
 within Fennoscandia and Italy. Ecology and Evolution, <i>in
 press</i>.
DOI: 10.5061/dryad.gxd2547nv
title: Interactions with soil fungi alter density-dependence and neighborhood effects in a locally abundant dipterocarp species

description: Seedling recruitment can be strongly affected by the composition of nearby
 plant species. At the neighborhood scale (on the order of tens of meters),
 adult conspecifics can modify soil chemistry and presence of host microbes
 (pathogens and mutualists) across their combined canopy area or rooting
 zones. At local or small spatial scales (on the order of one to few
 meters), conspecific seed or seedling density can influence the strength
 of intraspecific light and resource competition and also modify the
 density-dependent spread of natural enemies such as pathogens or
 invertebrate predators. Intrinsic correlation between proximity to adult
 conspecifics (i.e. recruitment neighborhood) and local seedling density,
 arising from dispersal, make it difficult to separate the independent and
 interactive factors that contribute to recruitment success. 
 Here, we present a field experiment in which we manipulated both the
 recruitment neighborhood and seedling density to explore how they interact
 to influence the growth and survival of Dryobalanops aromatica, a dominant
 ectomycorrhizal tree species in a Bornean tropical rainforest. First, we
 found that both local seedling density and recruitment neighborhood had
 effects on performance of D. aromatica seedlings, though the nature of
 these impacts varied between growth and survival. Second, we did not find
 strong evidence that the effect of density on seedling survival is
 dependent on the presence of conspecific adult trees. However,
 accumulation of mutualistic fungi beneath conspecifics adults does
 facilitate establishment of D. aromatica seedlings. In total, our results
 suggest that recruitment near adult conspecifics was not associated with a
 performance cost and may have weakly benefitted recruiting seedlings.
 Positive effects of conspecifics may be a factor facilitating the regional
 hyperabundance of this species.  Synthesis: Our results provide
 support for the idea that dominant species in diverse forests may escape
 the localized recruitment suppression that limits abundance in rarer
 species.
DOI: 10.5061/dryad.mpg4f4r1r
title: Model and data for: Economical defense of resources structures territorial space use in a cooperative carnivore

description: Manuscript Abstract: Ecologists have long sought to understand space use
 and mechanisms underlying patterns observed in nature. We developed an
 optimality landscape and mechanistic territory model to understand
 mechanisms driving space use and compared model predictions to empirical
 reality. We demonstrate our approach using gray wolves (Canis lupus). In
 the model, simulated animals selected territories to economically acquire
 resources by selecting patches with greatest value, accounting for
 benefits, costs, and tradeoffs of defending and using space on the
 optimality landscape. Our approach successfully predicted and explained
 first- and second-order space use of wolves, including the population’s
 distribution, territories of individual packs, and influences of prey
 density, competitor density, human-caused mortality risk, and seasonality.
 It accomplished this using simple behavioral rules and limited data to
 inform the optimality landscape. Results contribute evidence that
 economical territory selection is a mechanistic bridge between space use
 and animal distribution on the landscape. This approach and resulting
 gains in knowledge enable predicting effects of a wide range of
 environmental conditions, contributing to both basic ecological
 understanding of natural systems and conservation. We expect this approach
 will demonstrate applicability across diverse habitats and species, and
 that its foundation can help continue to advance understanding of spatial
 behavior. Model & Data Abstract: In support of the above
 manuscript, all model files and data to re-create the analyses for the
 manuscript are included on Dryad. The model can be run in NetLogo
 (installation file included), using the associated input files to build
 the Montana landscape for wolves. Expertise in NetLogo is strongly
 recommended for using this model. Output files are likewise included along
 with code to create each plot in the manuscript and SI. Software
 files for the model and code to create each plot in the manuscript are
 located at Zenodo: https://doi.org/10.5281/zenodo.5802243.
description: All details are provided in the Sells et al. Supplementary
 Information file.
DOI: 10.5061/dryad.x95x69pkk
title: Data from: Seeing the Forest for the trees: Assessing genetic offset predictions from Gradient Forest

description: Gradient Forest (GF) is a machine learning algorithm designed to analyze
 spatial patterns of biodiversity as a function of environmental gradients.
 An offset measure between the GF predicted environmental association of
 adapted alleles and a new environment (GF Offset), is increasingly being
 used to predict the loss of environmentally adapted alleles under rapid
 environmental change, but remains mostly untested for this purpose. Here
 we explore the robustness of GF Offset to assumption violations, and its
 relationship to measures of fitness, using SLiM simulations with explicit
 genome architecture and a spatial metapopulation. We evaluate measures of
 GF Offset in: (1) a neutral model with no environmental adaptation; (2) a
 monogenic “population genetic” model with a single environmentally adapted
 locus; and (3) a polygenic “quantitative genetic” model with two adaptive
 traits, each adapting to a different environment. We found GF Offset to be
 broadly correlated with fitness offsets under both single locus and
 polygenic architectures. However, neutral demography, genomic
 architecture, and the nature of the adaptive environment can all confound
 relationships between GF Offset and fitness. GF Offset is a promising
 tool, but it is important to understand its limitations and underlying
 assumptions, especially when used in the context of predicting
 maladaptation.
DOI: 10.5061/dryad.rbnzs7hcm
title: Disentangling the roles of plant functional diversity and plaint traits in regulating plant nitrogen accumulation and denitrification in freshwaters

description: 1. There is a growing recognition that functional measures of diversity,
 based on quantification of functionally important species traits, are
 useful for explaining variation in ecosystem processes. However, the
 mechanisms linking functional diversity to different processes remain
 poorly understood, hindering development of a predictive framework for
 ecosystem functioning based on species traits. 2. The current
 understanding of how the functional traits of aquatic plants (macrophytes)
 affect nitrogen (N) cycling by regulating microbial communities and their
 activity in freshwater habitats is particularly limited. Denitrifying
 bacteria are typically associated with the roots of both aquatic and
 terrestrial plants and denitrification is the main cause of loss of N from
 ecosystems. Disentangling the interplay between plants and microbial
 denitrifiers is key to understanding variation in rates of denitrification
 from local to landscape scales. 3. In a mesocosm experiment, we varied the
 species richness (monocultures or two- species mixtures) and composition
 of macrophytes. We quantified effects of both macrophyte functional
 diversity, quantified as functional trait dissimilarity, and functional
 trait composition, quantified as community weighted mean trait values, on
 N removal in wetlands. We used structural equation modelling to
 disentangle the direct and indirect influences of traits on N accumulation
 in plant biomass, denitrification activity and abundance of key bacterial
 denitrification genes (nirSand nirK). 4. Both functional
 diversity and functional trait composition regulated N removal, explaining
 70 – 94% variation in the underlying ecosystem processes. Increased
 macrophyte functional diversity increased plant N accumulation, and
 indirectly enhanced denitrification by increasing denitrification gene
 abundance. Among traits, greater plant relative growth rates, specific
 leaf area and aboveground biomass increased plant N accumulation.
 Denitrification activity increased with increasing belowground biomass but
 decreased with increasing root diameter. 5. These findings improve our
 understanding of N removal in freshwater wetlands dominated by
 macrophytes, and have broad ecological implications for wetland management
 targeting enhanced ecosystem services. Our results highlight the potential
 for optimising denitrification and plant N accumulation in wetlands and
 thereby improving water purification by increasing macrophyte functional
 diversity and ensuring the presence of key traits in macrophyte
 assemblages.
DOI: 10.5061/dryad.c59zw3r8t
title: Data from: Parasite-associated mortality in birds: the roles of specialist parasites and host evolutionary distance

description: The factors that influence whether a parasite is likely to cause death in
 a given host species are not well known. Generalist parasites with high
 local abundances, broad distributions, and the ability to infect a wide
 phylogenetic diversity of hosts are often considered especially dangerous
 for host populations, though comparatively little research has been done
 on the potential for specialist parasites to cause host mortality. Here,
 using a novel database of avian mortality records, we tested whether
 phylogenetic host specialist or host generalist haemosporidian blood
 parasites were associated with avian host deaths based on infection
 records from over 81,000 examined hosts. In support of the hypothesis that
 host specialist parasites can be highly virulent in novel hosts, we found
 that the parasites that were associated with avian host mortality were
 predominantly phylogenetic host specialists. Hosts that died tended to be
 distantly related to the host species that a parasite lineage typically
 infects, illustrating that specialist parasites can cause death outside of
 their limited host range. Overall, this study highlights the overlooked
 potential for host specialist parasites to cause host mortality despite
 their constrained ecological niches.
DOI: 10.5061/dryad.1rn8pk0vr
title: Data from: Predicting and measuring decision rules for social recognition in a Neotropical frog

description: Many animals use signals to recognize familiar individuals but risk
 mistakes because the signal properties of different individuals often
 overlap. Further, outcomes of correct and incorrect decisions yield
 different fitness payoffs, and animals incur these payoffs at different
 frequencies depending on interaction rates. To understand how signal
 variation, payoffs, and interaction rates shape recognition decision
 rules, we studied male golden rocket frogs, which recognize the calls of
 territory neighbors and are less aggressive to neighbors than to
 strangers. We first quantified patterns of individual variation in call
 properties and predicted optimal discrimination thresholds using signal
 variation. We then measured thresholds for discriminating between
 neighbors and strangers using a habituation-discrimination field playback
 experiment. Territorial males discriminated between calls differing by 9%
 to 12% in temporal properties, slightly higher than the predicted
 thresholds (5-10%). Finally, we used a signal detection theory model to
 explore payoff and interaction rate parameters and found that the
 empirical threshold matched those predicted under ecologically realistic
 assumptions of infrequent encounters with strangers and relatively costly
 missed detections of strangers. We demonstrate that receivers group
 continuous variation in vocalizations into discrete social categories and
 that signal detection theory can be applied to understand evolved decision
 rules.
description: See paper for methods.
description: See README file.
DOI: 10.5061/dryad.2rbnzs7pq
title: Mini-acoustic sensors reveal occupancy and threats to koalas (Phascolarctos cinereus) in private native forests

description: 1. Forests on private land have a wide range of uses that span activities
 such as recreation, primary production and nature conservation.
 Traditionally, it has been difficult for researchers to access private
 land to undertake systematic surveys. We used mini-acoustic sensors
 (Audiomoth) mailed via the postal service to overcome landholder concerns
 about researchers accessing private property, with a focus on properties
 used for private native forestry. 2. We surveyed koalas, an iconic
 threatened marsupial, in north-east New South Wales, Australia using
 passive acoustics, with repeat surveys over consecutive nights to account
 for imperfect detection in an occupancy modelling framework. 3. Over three
 years, we surveyed 128 sites and recorded 2,560 male bellows. Detection
 probability over seven nights was high (&gt;0.79), but varied
 substantially between years, due to use of different sensors, housings and
 weather conditions. After accounting for detection probability, modelling
 revealed that koalas commonly occupied private native forests of the study
 region (probability of occupancy = 0.58±0.08). 4. Occupancy was modelled
 against several covariates and it varied with the landscape extent of
 sealed roads (-ve), NDVI (-ve) and a habitat suitability model (+ve, but
 minor). There was no support for occupancy in private forests to be
 related to a range of other factors including extent of surrounding
 cleared land, timber harvesting history, fire and other measured habitat
 features. 5. Synthesis and applications. We conclude that mini-acoustic
 recorders mailed to landholders were a highly effective method for
 assessing koala occupancy on private land and the approach could be
 deployed more widely for a range of species. Private native forests in
 partly cleared landscapes are commonly occupied by koalas, highlighting
 that practices seeking to balance conservation and production should be
 encouraged.
DOI: 10.5061/dryad.m0cfxpp56
title: Data for: Heterosigma akashiwo transcriptome gene annotations

description: Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga
 (class: Raphidophyceae), and produces fish-killing blooms. There is a
 substantial scientific and practical interest in its ecophysiological
 characteristics that determine bloom dynamics and its adaptation to broad
 climate zones. A well-annotated genomic/genetic sequence information
 enables researchers to characterize organisms using modern molecular
 technology. In the present study, we conducted H. akashiwo RNA sequencing,
 a de novo transcriptome assembly of 84,693,530 high-quality deduplicated
 short-read sequences. The obtained RNA reads were assembled by
 Trinity assembler and 144,777 contigs were identified with N50 values of
 1085. The raw data were deposited in the NCBI SRA database (BioProject
 PRJDB6241 and PRJDB15108), and the assemblies are available in NCBI TSA
 database (ICRV01).  Total 60,877 open reading frames with the
 length of 150 bp or greater were predicted. Here, the top Gene Ontology
 terms, the pfam hits, and the BLAST hits were annotated for all the
 predicted genes, and shared as text files.
description: For functional characterization of the predicted gene models,
 the transcriptome (ICRV01,
 ICRV01000001-ICRV01144777, https://www.ncbi.nlm.nih.gov/Traces/wgs/ICRV01)
 was subjected to gene ontology (GO) analysis, BLASTP search, and Pfam
 domain search.<br>The GO terms were assigned to the predicted
 peptides in a two-step process. First, the best-match homologs of
 the<em> H. akashiwo</em> peptides were identified following a
 BLASTP search (E-value&lt;1) of a custom database composed of RefSeq
 gene models of <em>Arabidopsis thaliana</em>, <em>Homo
 sapiens</em>, <em>Mus musculus</em>,
 and <em>Saccharomyces cerevisiae </em>(S288C). Second,
 the <em>H. akashiwo</em> peptides were annotated with the GO
 terms (http://geneontology.org) assigned to their best-match homologs. The Pfam database (http://pfam.xfam.org) was used to predict the domains in the <em>H. akashiwo </em>gene models.
description: The provided data are all in text format.
DOI: 10.5061/dryad.80gb5mks6
title: Multidecadal, continent-level analysis indicates agricultural practices impact wheat aphid loads more than climate change

description: Temperature has a large influence on insect abundances, thus under climate
 change, identifying major drivers affecting pest insect populations is
 critical to world food security and agricultural ecosystem health. Here,
 we conducted a meta-analysis with data obtained from 120 studies across
 China and Europe from 1970 to 2017 to reveal how climate and agricultural
 practices affect populations of wheat aphids. Here we showed that aphid
 loads on wheat had distinct patterns between these two regions, with a
 significant increase in China but a decrease in Europe over this time
 period. Although temperature increased over this period in both regions,
 we found no evidence showing climate warming affected aphid loads. Rather,
 differences in pesticide use, fertilization, land use, and natural enemies
 between China and Europe may be key factors accounting for differences in
 aphid pest populations. These long-term data suggest that agricultural
 practices impact wheat aphid loads more than climate warming. 
description: We used
 regression analyses to examine how the abundance of aphids (log
 transformed) depended on year separately for each ~ten-day period in which
 aphids were present at least at some of the sites (March to May for China
 and May to July for Europe). To control for multiple points from the same
 study, we used the average value for each study for each year and ten-day
 period. We performed another set of regressions to examine how the
 abundance of natural enemies depended on year separately for each ten-day
 period in which they were present at least at some of the sites in China
 (April to May). In these analyses, we treated each 10-day time period
 separately and used averages for each year and 10-day period. We used the
 slopes of regressions to test for differences between the temporal pattern
 of change over years between China and Europe and among early, mid and
 late season aphid abundances in China and Europe. We considered an effect
 to be significant when the 95% CI did not overlap zero and we considered
 two intervals to be different when their 95% CIs did not overlap. We
 tested whether a country or provinces rate of change in aphid loads was
 correlated with its rate of change in temperature. We performed a mixed
 model ANOVA to test whether the proportion of area under cultivation
 depended on year for China provinces vs. European countries and used slope
 contrasts to test whether the slopes for China vs. Europe differed on
 average. We also tested whether slopes for individual countries or
 provinces differed from zero.
description: The software of word and Excel could open the data files.
DOI: 10.5061/dryad.8cz8w9grq
title: Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)

description: Background and Aims Rhododendron is a species-rich and taxonomically
 challenging genus due to recent adaptive radiation and frequent
 hybridization. A well-resolved phylogenetic tree would help to understand
 the diverse history of Rhododendron in the Himalaya–Hengduan
 Mountains where the genus is most diverse. Methods We reconstructed the
 phylogeny based on plastid genomes with broad taxon sampling,
 covering 161 species representing all eight subgenera and all 12
 sections, including ~45 % of the Rhododendron species native to
 the Himalaya–Hengduan Mountains. We compared this phylogeny with nuclear
 phylogenies to elucidate reticulate evolutionary events and
 clarify relationships at all levels within the genus. We
 also estimated the timing and diversification history of
 Rhododendron, especially the two species-rich
 subgenera Rhododendron and Hymenanthes that comprise &gt;90 %
 of Rhododendron species in the Himalaya–Hengduan Mountains. Key
 Results The full plastid dataset produced a well-resolved and supported
 phylogeny of Rhododendron. We identified 13 clades that were almost always
 monophyletic across all published phylogenies. The conflicts between
 nuclear and plastid phylogenies strongly suggested that reticulation
 events may have occurred in the deep lineage history of the
 genus. Within Rhododendron, subgenus Therorhodion diverged first at 56
 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya,
 generating ten lineages among the component 12 clades of
 core Rhododendron. Diversification in subgenus Rhododendron
 accelerated c. 16.6 Mya and then became fairly
 continuous. Conversely, Hymenanthes diversification was slow at
 first, then accelerated very rapidly around 5 Mya. In the
 Himalaya–Hengduan Mountains, subgenus Rhododendron contained one major
 clade adapted to high altitudes and another to low altitudes,
 whereas most clades in Hymenanthes contained both low- and high-altitude
 species, indicating greater ecological plasticity during its
 diversification. Conclusions The 13 clades proposed here may help to
 identify specific ancient hybridization events. This study will
 help to establish a stable and reliable taxonomic framework for
 Rhododendron, and provides insight into what drove its
 diversification and ecological adaption. Denser sampling of taxa,
 examining both organelle and nuclear genomes, is needed to better
 understand the divergence and diversification history
 of Rhododendron.