cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.td356
title: Data from: Host nuclear genotype influences phenotype of a conditional mutualist symbiont

description: Arthropods commonly carry maternally-inherited intracellular bacterial
 symbionts that may profoundly influence host biology and evolution. The
 intracellular symbiont Rickettsia sp. nr. bellii swept rapidly into
 populations of the sweetpotato whitefly Bemisia tabaci in the southwestern
 USA. Previous laboratory experiments showed female-bias and fitness
 benefits were associated with Rickettsia infection, potentially explaining
 the high frequencies of infection observed in field populations, but the
 effects varied with whitefly genetic line. Here we explored whether host
 extranuclear or nuclear genes influenced the variation in the
 Rickettsia-host phenotype in two genetic lines of the whitefly host, each
 with Rickettsia-infected and uninfected sublines. Introgression between
 the Rickettsia-infected subline of one genetic line and the
 Rickettsia-uninfected subline of the other was used to create two new
 sublines, each with the maternally-inherited extranuclear genetic lineages
 of one line (Rickettsia, two other symbionts and the mitochondria) and the
 nuclear genotype of the other. Performance assays comparing the original
 and new lines showed that in addition to Rickettsia, the interaction of
 Rickettsia infection with host nuclear genotype influenced development
 time and the sex ratio of the progeny, while the extranuclear genotype did
 not. Host nuclear genotype, but not extranuclear genotype, also influenced
 the titer of Rickettsia. Our results support the hypothesis that
 differences in host nuclear genotype alone may explain considerable
 within-population variation in host-symbiont phenotype, and may contribute
 to the observed variation in Rickettsia-whitefly interactions worldwide.
description: Hunter_JEB_2016_Hostgenotype_TotalprogenyThese are the data used for the total progeny analysis presented in figure 2.Hunter_JEB_2016_Hostgenotype_Sex_ratiosThese are the sex ratio data used for figure 4. Refer to the manuscript text for descriptions of treatments etc.Hunter_JEB_2016_Hostgenotype_Develop_timeThese are the data used for the development time analysis (Fig. 3 a and b).Hunter_JEB_2016_Hostgenotype_RickettsiatiterThese are the estimates of Rickettsia titer relative to actin titer among the 4 Rickettsia-infected treatments. (Fig. 5)
DOI: 10.5061/dryad.h3j360r
title: Data from: Incubation temperature and social context affect the nest exodus of precocial ducklings

description: The environments that animals experience during development have important
 fitness consequences. In birds, parents influence the developmental
 environment of their offspring through incubation. Subtle changes in
 incubation temperature affect offspring morphology and physiology, such as
 growth, immune function, and thermoregulation, yet little is known about
 how it may affect critical early-life behaviors. Because expression of
 behavior can be influenced by the social environment, the effect of
 incubation temperature on behavior may be context-dependent. We
 investigated whether incubation temperature and social context influence a
 critical early-life task in wood ducks (Aix sponsa). Wood ducks nest in
 tree cavities and, shortly after hatching, ducklings must jump and climb
 out of the cavity. Failure to exit the nest is fatal. In two experiments,
 we incubated eggs at different mean temperatures and examined the nest
 exodus of ducklings individually and in mixed-incubation temperature
 pairs. When tested individually, ducklings incubated at 35.8°C and 37.0°C
 were ~2.5 times more successful at exiting the nest, and jumped and
 climbed more often, than those incubated at 35.0°C. However, in an
 experiment conducted the following year, we found that social interactions
 mitigated these effects and there was no difference in nest exodus success
 when ducklings incubated at 35.0°C and 36.0°C were tested together in
 pairs. This may be because, when in pairs, ducklings incubated at the low
 temperature experience social enhancement while those incubated at the
 high temperature maintain similar behaviors. These results advance our
 understanding of how parental effects influence offspring behaviors and
 performance within different social contexts.
description: Nest Exodus
 DataThis data was collected
 during two experiments that examined the effect of incubation temperature
 on the nest exodus behavior of wood duck ducklings. Wood duck eggs were
 collected from nest boxes at the Savannah River Site in South Carolina,
 USA. Eggs were incubated and experiments were conducted at Virginia Tech.
 The zip file contains two Excel spreadsheets. One is data from the
 Individual Experiment, where ducklings were tested on their ability to
 exit a nest box individually. The other is data from the Pairs Experiment,
 where ducklings were tested in mixed incubation temperature
 pairs.
DOI: 10.5517/ccdc.csd.cc2qs12n
title: CCDC 2525541: Experimental Crystal Structure Determination

description: Related Article: Yanhui Zhao|2026|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.0g0t0
title: Data from: Bark beetles attacking conifer seedlings: picking on the weakest or feasting upon the fittest?

description: 1. Plant stress from causes such as drought is thought to increase the
 susceptibility of plants to herbivore attack and damage. Although this
 forms the basis of the widely cited plant stress hypothesis, there are few
 cases where this has been tested thoroughly. 2. We compared the frequency
 of attack and damage of an invasive pine bark beetle Hylates ater, on
 seedlings of Pinus radiata, using a 2×2 factorial design with artificially
 induced stress and insecticide application to distinguish effects of
 beetle attack and direct effects of stress. 3. Contrary to expectations
 based on the plant stress hypothesis, twice as many unstressed seedlings
 (22%) were attacked than stressed seedlings (11%). However, stressed
 seedlings were twice as likely to experience sustained bark beetle feeding
 resulting in girdling, than unstressed seedlings (31% and 15%,
 respectively). 4. In response to beetle attack, unstressed seedlings
 showed much stronger resin production than stressed seedlings, which is
 likely to explain the greater survival of unstressed seedlings after
 attack. 5. Experimental drought stress caused a 50% reduction in shoot
 growth. 6. Synthesis and applications. Maximising seedling vigour and
 minimising (pre-)planting stress are key for the resilience of planted
 forests. Managers should emphasise a stress-free transition of seedlings
 from nursery to field as well as correct planting techniques, in order to
 safeguard this vulnerable stage. This is particularly crucial since
 drought stress and insect invasions are likely to increase as a result of
 global change.
description: Hylastes_dataPrimary data setFig_1_dataPhenology dataTable_S1_Hylastes_damage_summary_SuppInfoSupplementary information - seedling damage survey - table of resultsAppendix_S1_Hylastes_damage_survey_SuppInfoSupplementary information - seedling damage survey
DOI: 10.5061/dryad.t2d38
title: Data from: Displayed trees do not determine distinguishability under the network multispecies coalescent

description: Recent work in estimating species relationships from gene trees has
 included inferring networks assuming that past hybridization has occurred
 between species. Probabilistic models using the multispecies coalescent
 can be used in this framework for likelihood-based inference of both
 network topologies and parameters, including branch lengths and
 hybridization parameters. A difficulty for such methods is that it is not
 always clear whether, or to what extent, networks are identifiable-that is
 whether there could be two distinct networks that lead to the same
 distribution of gene trees. For cases in which incomplete lineage sorting
 occurs in addition to hybridization, we demonstrate a new representation
 of the species network likelihood that expresses the probability
 distribution of the gene tree topologies as a linear combination of gene
 tree distributions given a set of species trees. This representation makes
 it clear that in some cases in which two distinct networks give the same
 distribution of gene trees when sampling one allele per species, the two
 networks can be distinguished theoretically when multiple individuals are
 sampled per species. This result means that network identifiability is not
 only a function of the trees displayed by the networks but also depends on
 allele sampling within species. We additionally give an example in which
 two networks that display exactly the same trees can be distinguished from
 their gene trees even when there is only one lineage sampled per species.
description: SupplementSupplemental Tables 1-3 for the paper.
DOI: 10.5061/dryad.8hj8t
title: Data from: Phytoplankton community interactions and environmental sensitivity in coastal and offshore habitats

description: Assessing the relative importance of environmental conditions and
 community interactions is necessary for evaluating the sensitivity of
 biological communities to anthropogenic change. Phytoplankton communities
 have a central role in aquatic food webs and biogeochemical cycles,
 therefore, consequences of differing community sensitivities may have
 broad ecosystem effects. Using two long-term time series (28 and 20 years)
 from the Baltic Sea, we evaluated coastal and offshore major phytoplankton
 taxonomic group biovolume patterns over annual and monthly time-scales and
 assessed their response to environmental drivers and biotic interactions.
 Overall, coastal phytoplankton responded more strongly to environmental
 anomalies than offshore phytoplankton, although the specific environmental
 driver changed with time scale. A trend indicating a state shift in annual
 biovolume anomalies occurred at both sites and the shift's timing at
 the coastal site closely tracked other long-term Baltic Sea ecosystem
 shifts. Cyanobacteria and the autotrophic ciliate Mesodinium rubrum were
 more strongly related than other groups to this trend with opposing
 relationships that were consistent across sites. On a monthly scale,
 biotic interactions within communities were rare and did not overlap
 between the coastal and offshore sites. Annual scales may be better able
 to assess general patterns across habitat types in the Baltic Sea, but
 monthly community dynamics may differ at relatively small spatial scales
 and consequently respond differently to future change.
description: DFA_dataThis zip file contains the phytoplankton and covariate data for conducting the dynamic factor analyses (DFA).MARSS_dataThis file contains the phytoplankton and covariate data for conducting the species interaction analyses using the MARSS framework.
DOI: 10.5281/zenodo.17257884
title: Lung-associated_vOTU
DOI: 10.5061/dryad.2dj32
title: Data from: Evidence for shifts to faster growth strategies in the new ranges of invasive alien plants

description: Understanding the processes underlying the transition from introduction to
 naturalisation and spread is an important goal of invasion ecology.
 Release from pests and pathogens in association with capacity for rapid
 growth are thought to confer an advantage for species in novel regions. We
 assessed leaf herbivory and leaf-level traits associated with growth
 strategy in the native and exotic ranges of 13 invasive plant species from
 256 populations. Species were native to either the Western Cape region of
 South Africa, south-western Australia, or south-eastern Australia and had
 been introduced to at least one of the other regions or to New Zealand. We
 tested for evidence of herbivore release and shifts in leaf traits between
 native and exotic ranges of the 13 species. Across all species, leaf
 herbivory, specific leaf area and leaf area were significantly different
 between native and exotic ranges while there were no significant
 differences across the 13 species found for leaf mass, assimilation rate,
 dark respiration or foliar nitrogen. Analysis at the species- and
 region-level showed that eight out of 13 species had reduced leaf
 herbivory in at least one exotic region compared to its native range. Six
 out of 13 species had significantly larger specific leaf area (SLA) in at
 least one exotic range region and 5 of those 6 species experienced reduced
 leaf herbivory. Increases in SLA were underpinned by increases in leaf
 area rather than reductions in leaf mass. No species showed differences in
 the direction of trait shifts from the native range between different
 exotic regions. This suggests that the driver of selection on these traits
 in the exotic range is consistent across regions, and hence is most likely
 to be associated with factors linked with introduction to a novel
 environment, such as release from leaf herbivory, rather than with
 particular environmental conditions. Synthesis: These results provide
 evidence that introduction of a plant species into a novel environment
 commonly results in a reduction in the top-down constraint imposed by
 herbivores on growth, allowing plants to shift towards a faster growth
 strategy which may result in an increase in population size and spread and
 consequently to invasive success.
description: Leaf trait data for
 native and exotic rangesData of leaf traits for
 13 invasive species collected in their native and exotic
 rangesLeishman Cooke
 Richardson.csv
DOI: 10.5061/dryad.7nc75
title: Data from: Invasive Asian earthworms negatively impact keystone terrestrial salamanders

description: Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp.) are
 invading North American forests and consuming the vital detrital layer
 that forest floor biota [including the keystone species Plethodon cinereus
 (Eastern Red-backed Salamander)], rely on for protection, food, and
 habitat. Plethodon cinereus population declines have been associated with
 leaf litter loss following the invasion of several exotic earthworm
 species, but there have been few studies on the specific interactions
 between pheretimoid earthworms and P. cinereus. Since some species of
 large and active pheretimoids spatially overlap with salamanders beneath
 natural cover objects and in detritus, they may distinctively compound the
 negative consequences of earthworm-mediated resource degradation by
 physically disturbing important salamander activities (foraging, mating,
 and egg brooding). We predicted that earthworms would exclude salamanders
 from high quality microhabitat, reduce foraging efficiency, and negatively
 affect salamander fitness. In laboratory trials, salamanders used lower
 quality microhabitat and consumed fewer flies in the presence of
 earthworms. In a natural field experiment, conducted on salamander
 populations from “non-invaded” and “pheretimoid invaded” sites in Ohio,
 salamanders and earthworms shared cover objects ~60% less than expected.
 Earthworm abundance was negatively associated with juvenile and male
 salamander abundance, but had no relationship with female salamander
 abundance. There was no effect of pheretimoid invasion on salamander body
 condition. Juvenile and non-resident male salamanders do not hold stable
 territories centered beneath cover objects such as rocks or logs, which
 results in reduced access to prey, greater risk of desiccation, and
 dispersal pressure. Habitat degradation and physical exclusion of
 salamanders from cover objects may hinder juvenile and male salamander
 performance, ultimately reducing recruitment and salamander abundance
 following Asian earthworm invasion.
description: Ziemba et al. 2016 Lab
 and Field DataLaboratory and field
 data for experiments examining the interactions between invasive Asian
 earthworms and terrestrial salamanders in northeastern Ohio,
 USA.Ziemba_et_al_2016.xlsx
DOI: 10.5061/dryad.99dc0
title: Data from: Multiresponse algorithms for community-level modeling: review of theory, applications, and comparison to species distribution models

description: 1.Community-level models (CLMs) consider multiple, co-occurring species in
 model fitting and are lesser known alternatives to species distribution
 models (SDMs) for analyzing and predicting biodiversity patterns. CLMs
 simultaneously model multiple species, including rare species, while
 reducing overfitting and implicitly considering drivers of co-occurrence.
 Many CLMs are direct extensions of well-known SDMs and therefore should be
 familiar to ecologists. However, CLMs remain underutilized, and there have
 been few tests of their potential benefits and no systematic reviews of
 their assumptions and implementations. Here we review this emerging field
 and provide examples in R to fit common CLMs. Our goal is to introduce
 CLMs to a broader audience, and discuss their attributes, benefits, and
 limitations relative to SDMs. 2.We review i) statistical implementations
 and applications of CLMs, ii) their advantages and limitations, and iii)
 comparative analyses of CLMs and SDMs. We also suggest directions for
 future research. 3.We identify seven CLM algorithms with similar data
 structures and predictive outputs as SDMs that should be most accessible
 to ecologists familiar with species-level modeling, including five methods
 that predict assemblage composition and individual species distributions
 and two methods that model compositional turnover along environmental
 gradients. CLMs have been applied to numerous taxa, regions, and spatial
 scales, and a variety of topics (e.g., studying drivers of community
 structure or assessing relationships between community composition and
 functional traits). Studies suggest that the relative benefits of CLMs and
 SDMs may be case specific, especially in terms of predicting species
 distributions and community composition. However, CLMs may offer
 advantages in terms of computational efficiency, modeling rare species,
 and projecting to no-analog climates. A major shortcoming of CLMs is their
 reliance on presence-absence community composition data. 4.Studies are
 needed to assess the relative merits of SDMs and CLMs, and different CLM
 algorithms, with a focus on three key areas: i) under which circumstances
 CLMs improve predictions for rare species, ii) how CLMs perform under
 different community compositions (e.g. relative abundance of rare vs.
 common species), including the extent to which co-occurrence patterns are
 structured by biotic interactions, and iii) ability to project across
 time/space.
description: Studies applying
 Community Level ModelsSummary table of
 empirical studies applying Community Level Models (CLMs). The studies have
 been grouped by CLM algorithm.CLMs_review-Dryad-Data.xlsxCommunity Level Modeling vignetteRmarkdown file with code for the Community Level Modeling tutorial: Fitting multispecies models in RCLMs_review-Dryad-Code.Rmd
DOI: 10.5061/dryad.1435
title: Data from: Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes

description: Chromosome rearrangements may affect the rate and patterns of gene flow
 within species, through reduced fitness of structural heterozygotes or by
 reducing recombination rates in rearranged areas of the genome. While the
 effects of chromosome rearrangements on gene flow have been studied in a
 wide range of organisms with monocentric chromosomes, the effects of
 rearrangements in holocentric chromosomes—chromosomes in which centromeric
 activity is distributed along the length of the chromosome—have not. We
 collected chromosome number and molecular genetic data in Carex scoparia,
 an eastern North American plant species with holocentric chromosomes and
 highly variable karyotype (2n = 56–70). There are no deep genetic breaks
 within C. scoparia that would suggest cryptic species differentiation.
 However, genetic distance between individuals is positively correlated
 with chromosome number difference and geographic distance. A positive
 correlation is also found between chromosome number and genetic distance
 in the western North American C. pachystachya (2n = 74–81). These findings
 suggest that geographic distance and the number of karyotype
 rearrangements separating populations affect the rate of gene flow between
 those populations. This is the first study to quantify the effects of
 holocentric chromosome rearrangements on the partitioning of intraspecific
 genetic variance.
description: R workspace with all
 Carex pachystachya dataR workspace with Carex
 pachystachya genetic and chromosome data, and geographic coordinates. Load
 into R using the "load" command. Two objects are contained in
 the workspace: (1) a table named "coordAndChrom3" that contains
 Whitkus's voucher numbers, diploid chromosome counts, and decimal
 latitude and longitude for each population; and (2)
 "whitkusFinal", a list of two matrices, the first a matrix of
 allele frequencies indexed by locus (rows) and population (columns), the
 second a matrix of sample sized indexed in the same
 manner.whitkusData.RdataZip file to conduct Carex scoparia analyses in RA zip file with an R workspace and a source file that executes all analyses conducted in R to generate Table 2. To execute, unzip the files into your working directory, load the file called "scopariaWorkspace.Rdata" into R, then source the file called "27may08analyses.R". Please note that the mantel tests are set to run for 200 permutations in this file, to make life easy when you are running... these mantel tests were actually run for 20,000 permutations for the final paper. Please email me if you have trouble running this.scoparia-R-analyses.zipNEXUS file for Carex scoparia and outgroupsA nexus file for Carex scoparia and outgroups. Original binned data are in a separate file.aflp_30march08_corrected-withPaupEnd.nex