cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tdz08kq0p
title: Lineage-specific variation in the evolutionary stability of coral photosymbiosis.

description: Over half of reef-building corals (Scleractinia) participate in a
 nutritional symbiosis, known as photosymbiosis, with photosynthetic
 dinoflagellates that ranges from obligate to facultative dependence.
 Fitting hidden-rates models allowing among-lineage variation in the rate
 of trait evolution to supertree and molecular phylogenies of Scleractinia,
 we reconstruct the history of photosymbiosis within Scleractinia and
 characterize its evolutionary stability. We find that most lineages of
 scleractinians are extraordinarily stable for the trait, evincing no
 instances of loss, but that in some clades photosymbiosis is more labile,
 thus providing a framework for comparative studies to further our
 mechanistic understanding of the factors that shape the evolutionary fates
 of scleractinian photosymbiosis.
DOI: 10.5061/dryad.cjsxksn65
title: Coverage data in males and females, and genetic markers used for genetic mapping of the guppy LG12 (sex chromosome pair)

description: The study used genetic mapping and coverage data in genome sequences of
 multiple male and female individuals of M. picta from multiple natural
 populations to investigate genetic degeneration of the Y chromosome, and
 quantify gene loss from the Y. The files include coverage results from the
 sex chromosome that were (i) used for sexing the sequenced individuals,
 and (ii) combined with autosomal results to analyze M/F, M/A and F/A depth
 of coverage ratios. Genetic mapping was also used to validate sex linkage,
 and the data set includes files with genotypes of genetic markers.
description: ​​​​​​The
 methods are described in detail in the PLoS Genetics paper, a manuscript
 that is currently in revision for Genome Biology and Evolution —
 GBE-210408.R1, and the unpublished paper, Bergero et al., 2019 (see
 reference above).
description: The readme
 file contains an explanation of each of the datasets. 
 NOTE: an assembly of the M. picta genome is available
 in the European Nucleotide Archive under accession number ERZ1744533
 (https://www.ebi.ac.uk/ena/browser/text-search?query=PRJEB43222).
DOI: 10.5061/dryad.6hdr7sr1g
title: Drivers of soil microbial community assembly during recovery from selective logging and clear cutting

description: Despite important progress in understanding the impacts of forest clearing
 and logging on aboveground communities, how these disturbances affect soil
 microbial β-diversity and the ecological processes driving microbial
 assemblages are poorly understood. Further, whether and how the microbial
 shifts affect vegetation composition and diversity during recovery of
 post-logged forests remain elusive. 2. Using a spatial grid experiment
 design in a primary tropical forest intermixed with post-logged patches
 naturally recovered for half century in Hainan Island, China, we
 characterized and explained the distance-decay relationships of soil
 microbial similarities in primary, selectively logged and clear cut
 forests. 3. Selectively logged sites showed a lower spatial turnover rate
 of bacterial assemblages based on phylogenetic and taxonomic β-diversity,
 but a higher spatial turnover rate of fungal assemblages based on
 phylogenetic β-diversity, suggesting a higher level of phylogenetic
 variability in fungal composition. Clear cut sites showed lower spatial
 turnover for both bacterial and fungal assemblages based on the two
 β-diversity, indicating community homogenization. Main drivers of
 microbial assemblages shifted from soil properties in primary forest to
 tree composition in selectively logged sites, whereas microbial-tree
 associations declined in clear cut sites, leading to stochastically
 organized microbial assemblages. 4. Synthesis and applications. The
 increased fungal phylogenetic turnover with tree turnover following
 selective logging promotes unassisted recovery of plant diversity. In
 contrast, the decoupling of tree and microbial turnover following
 clear-cutting suggests restoration approaches based on tree planting, and
 tree species that have strong associations with bulk soil microbial
 community should be considered. Our findings advance the understanding of
 spatial patterns, processes, and drivers of soil microbial assemblages in
 parallel with tree community recovery during regeneration of post-logged
 tropical forests, and highlight the importance of coupling assemblage
 patterns between tree and soil fungal communities for conserving tropical
 forest biodiversity.12-Jul-2021 --
DOI: 10.5061/dryad.5tb2rbp4g
title: Data from: Pulled diversification rates, lineages-through-time plots and modern macroevolutionary modelling

description: Estimating time-dependent rates of speciation and extinction from dated
 phylogenetic trees of extant species (timetrees), and determining how and
 why they vary, is key to understanding how ecological and evolutionary
 processes shape biodiversity. Due to an increasing availability of
 phylogenetic trees, a growing number of process-based methods relying on
 the birth-death model have been developed in the last decade to address a
 variety of questions in macroevolution. However, this methodological
 progress has regularly been criticised such that one may wonder how
 reliable the estimations of speciation and extinction rates are. In
 particular, using lineages-through-time (LTT) plots, a recent study (Louca
 & Pennell, 2020) has shown that there are an infinite number of
 equally likely diversification scenarios that can generate any timetree.
 This has led to questioning whether or not diversification rates should be
 estimated at all. Here we summarize, clarify, and highlight technical
 considerations on recent findings regarding the capacity of models to
 disentangle diversification histories. Using simulations we illustrate the
 characteristics of newly-proposed "pulled rates" and their
 utility. We recognize that the recent findings are a step forward in
 understanding the behavior of macroevolutionary modelling, but they in no
 way suggest we should abandon diversification modelling altogether. On the
 contrary, the study of macroevolution using phylogenetic trees has never
 been more exciting and promising than today. We still face important
 limitations in regard to data availability and methodological
 shortcomings, but by acknowledging them we can better target our joint
 efforts as a scientific community.
description: Fig2.R allows for the simulation of examples of unidentifiability
 in a simple dataset using an MCMC chain. MCMC.Rdata contains the
 associated files for an MCMC simulation run. Fig3.R and
 Fig4.R details the simulations of phylogenetic trees, LTT plots under
 scenarios of constant diversification rates and a single increase in
 speciation rate respectively. Corresponding simulation data can be found
 in constantRates.Rdata and rateShift.Rdata. Fig5.R
 provides code for simulating three different commonly-investigated
 scenarios of diversification rate change over time, and a final more
 complex and unrealistic scenario.
DOI: 10.5061/dryad.jq2bvq88z
title: Phenotypic plasticity may mediate habitat filtering in a forest edge community

description: A key process determining community assembly is habitat filtering, which
 reduces the range of trait values and thus leads to trait convergence.
 Habitat filtering is often assumed to involve a reduction in species
 richness, but such trait convergence could also result from phenotypic
 plasticity. By allowing more species in the community to show the “right”
 phenotype and pass the filter, phenotypic plasticity could maintain
 species richness despite trait convergence. If phenotypic plasticity plays
 this role, environmental changes should modify trait distribution but not
 species composition or richness. We tested this hypothesis in a forest
 edge community recently invaded by the alien shrub Rubus praecox. We
 measured functional traits beneath Rubus canopy (Rubus-invaded community)
 and in adjacent microsites naturally free from Rubus (original community),
 comparing trait dispersion and community structure parameters. We also
 characterized the microenvironments to seek functional explanations for
 the observed phenotypic changes. The functional dispersion parameter FDis
 showed habitat filtering in the Rubus-invaded community (trait
 convergence), while in the original community it did not differ from a
 null model. Species richness and composition did not differ between the
 two communities. Soil characteristics were similar in both communities but
 light availability was greatly reduced in the Rubus-invaded community. A
 Principal Component Analysis of community-weighted means of functional
 traits showed that phenotypic changes between communities were mostly
 consistent with functional responses to shading, including an increase in
 specific leaf area and a reduction in flavonoid concentration in the
 Rubus-invaded community. We verified the conditions necessary to infer
 that phenotypic plasticity mediates the outcome of habitat filtering
 driven by Rubus in the study system, i.e., plasticity would explain
 species persistence despite trait convergence. Phenotypic plasticity,
 often subsumed within intraspecific variation in community assembly
 studies, should be considered individually to improve our understanding of
 the causes and consequences of habitat filtering.
description: Trait Data – Functional
 traits measured in each block, per species, in both original and adjacent
 <i>Rubus</i>-invaded communities. Trait abbreviations as
 indicated in the text and in the legend of Figure 4. n/a: trait not
 measured. Community Data – Species presence
 and abundance in each block, in both original and adjacent
 <i>Rubus</i>-invaded communities. Soil Data – Soil parameters
 measured in each block, per species, in both original and adjacent
 <i>Rubus</i>-invaded communities. Trait abbreviations as
 indicated in the text and in the legend of Figure S1. Light Data – Photosynthetically
 active radiation (µmol m<sup>-2</sup>
 s<sup>-1</sup>) 5 cm above ground level in each block, in both
 original and adjacent <i>Rubus</i>-invaded
 communities.
DOI: 10.5061/dryad.ttdz08kzn
title: Novel disease state model finds most juvenile green turtles develop and recover from fibropapillomatosis

description: Fibropapillomatosis (FP) is a sea turtle disease characterized by benign
 tumor development on skin, eyes, and/or internal organs. It primarily
 affects juvenile green turtles (Chelonia mydas) in coastal foraging sites.
 The Indian River Lagoon (IRL), Florida, USA, is a coastal green turtle
 foraging site where the observed FP annual rate averaged 49% between 1983
 and 2018. FP is not a major cause of sea turtle mortality and most
 individuals fully recover; however, the overall dynamics of this disease
 are poorly understood because prior disease history is unknown for
 individuals without FP at capture time, and future disease outcome is
 unknown for individuals with FP at capture time. To better evaluate FP
 dynamics for green turtles in the IRL, we developed a hierarchical model
 for predicting disease state change. We used data from 4,149 captures of
 3,700 individual green turtles captured in the IRL. The hierarchical
 disease state model contained two levels: level one modeled whether an
 individual would develop FP, and level two modeled disease state
 progression, including states for pre-FP affliction, active FP affliction,
 and full recovery from FP. From the hierarchical model, we estimated 99.8%
 (95% credibility intervals 99.1-100%) of juvenile green turtles in the IRL
 developed FP, indicating that nearly every individual in the IRL is
 affected by this disease. The model also suggested that turtles quickly
 developed FP upon recruitment to the IRL and then recovered at different
 rates, with most completely recovering before emigrating from the IRL as
 they mature. This is the first analysis of long-term sea turtle data
 suggesting nearly every turtle in an aggregation both develops and
 recovers from FP.
description: Please refer to publication
description: The R code is uploaded to a text file. The Excel file with FP
 data includes the following column headers: EID =
 assigned identifyer FP = a binary list of whether a
 turtle had the tumor disease FP or not (0=no, 1=yes)
 FP_YESNO = whether a turtle had the tumor disease FP or not (Yes
 or No) Year = year that the sample was
 collected SCL = Straight Carapace Length of the turtle
 sampled (in centimeters) SCLbinned = the size bin that
 the turtle was included in based on 5 cm incrimental bins of SCL
 Season = the northern hemisphere season in which the turtle was
 sampled (Spring, Summer, Fall, or Winter) Columns with
 seasons broken out = binary list of 0 (not present) or 1 (present) for
 each season (for model purposes) y0, y1, y2 =
 presence/absence recaptures 0 - 2 years after the first encounter (0 = not
 present; 1 = present).
DOI: 10.15468/dl.ddm69z
title: Occurrence Download

description: A dataset containing 384 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Selenaspidus articulatus)"
 ]
}

 The dataset includes 384 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002893-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pk0p2ngp0
title: Improved nutritional status may promote an "asset protection" reproductive strategy in male rock lizards

description: Investing in the current reproduction requires diverting energy resources
 from other metabolic functions, which may compromise future reproduction
 and lifespan. To solve this trade-off, an individual may consider its
 labile state to decide how much to invest in current reproduction. We
 tested experimentally whether the "state quality" of male rock
 lizards influences their reproductive strategies. To improve the
 nutritional status of males before the mating season, we captured and
 supplemented experimental males (N = 20) with dietary vitamin D3 (an
 essential nutrient for lizards) and had a control group of males (N = 20).
 Then, we released all these males and females (N = 31) in a large
 semi-natural outdoor enclosure where lizards could interact and mate
 freely during the mating period. Activity levels of males did not vary
 between treatments, but supplemented males started fewer intrasexual
 agonistic interactions and made fewer mating advances to females. When the
 mating season ended, we incubated eggs laid by females to obtain the
 offspring and estimated the paternity of males using DNA microsatellites.
 Supplemented males sired fewer offspring than control males. These results
 suggest that vitamin D3 supplemented males used a low risk/less costly
 mating strategy to protect their assets (i.e. vitamin D reserves), but
 that still resulted in "some" current reproductive success,
 while likely increasing longevity and the expected future total
 reproductive success.
description: See readme file
DOI: 10.5061/dryad.0p2ngf21w
title: Data from: Genotypic traits and tradeoffs of fast growth in silver birch, a pioneer tree

description: Fast-growing and slow-growing plant species are suggested to show
 integrated economics spectrums and the tradeoffs of fast growth are
 predicted to emerge as susceptibility to herbivory and resource
 competition. We tested if these predictions also hold for fast-growing and
 slow-growing genotypes within a silver birch, Betula pendula population.
 We exposed cloned saplings of 17 genotypes with slow, medium or fast
 height growth to reduced insect herbivory, using an insecticide, and to
 increasing resource competition, using naturally varying field plot grass
 cover. We measured shoot and root growth, ectomycorrhizal (EM) fungal
 production using ergosterol analysis and soil N transfer to leaves using
 15N-labelled pulse of NH4+. We found that fast-growing genotypes grew on
 average 78% faster, produced 56% and 16% more leaf mass and ergosterol,
 and showed 78% higher leaf N uptake than slow-growing genotypes. The
 insecticide decreased leaf damage by 83% and increased shoot growth, leaf
 growth and leaf N uptake by 38%, 52% and 76%, without differences between
 the responses of fast-growing and slow-growing genotypes, whereas root
 mass decreased with increasing grass cover. Shoot and leaf growth of
 fast-growing genotypes decreased and EM fungal production of slow-growing
 genotypes increased with increasing grass cover. Our results suggest that
 fast growth is genotypically associated with higher allocation to EM
 fungi, better soil N capture and greater leaf production, and that the
 tradeoff of fast growth is sensitivity to competition, but not to insect
 herbivory. EM fungi may have a dual role: to support growth of
 fast-growing genotypes under low grass competition and to maintain growth
 of slow-growing genotypes under intensifying competition.
description: The dataset is from a field
 experiment, established in south Finland in 2009, where saplings of 17
 silver birch (<em>Betula pendula</em>) genotypes were
 subjected to an insecticide treatment and naturally varying resource
 competition by grasses through growing seasons 2010 and 2011. Shoot growth
 was used to assign the genotypes into three growth classes: slow, moderate
 and fast. Data of aboveground attributes (shoot growth, leaf mass, leaf N
 concentration, leaf herbivory damage, uptake of soil N and top shoot
 damage) and roots (root mass, root allocation index) are from summer 2011,
 while the data of extomycorrhizal fungal growth (estimated as ergosterol
 mass) was collected in both 2010 and 2011.
DOI: 10.5061/dryad.tdz08kq0q
title: Data from: A generalist nematode destabilizes plant competition: no evidence for direct effects, but strong evidence for indirect effects on rhizobia abundance

description: 1. Difficulties quantifying pathogen load and mutualist abundance limit
 our ability to connect disease dynamics to host community ecology. For
 example, specific predictions about how differential pathogen load is
 hypothesized to drive host competitive outcomes are rarely tested.
 Additionally, although infection is known to affect mutualists, we rarely
 measure the magnitude of pathogen effects on mutualist abundance across
 host competitive contexts. We tested for both mechanisms in a
 plant-rhizobia-nematode system. 2. We paired the legume Medicago lupulina
 with intra- and interspecific plant competitors, with and without a
 generalist nematode parasite Meloidogyne sp. Relative change in plant
 biomass was used to determine how nematode inoculation affected plant
 competitive outcomes. We counted nematode galls to test for direct effects
 of parasitism on plant competition, and rhizobia nodules to test for
 indirect effects of nematode presence on rhizobia abundance. 3. Parasites
 were destabilizing despite similar nematode load across competition
 treatments. During inter- compared to intraspecific competition, nematode
 inoculation decreased nodulation on M. lupulina, increased nodulation on
 Trifolium repens, and had no effect on nodulation on Chamaecrista
 fasciculata. 4. We found no support for hypothesized direct effects of
 nematode load on competitive outcomes, and strong but idiosyncratic
 indirect effects of nematode inoculation on rhizobia abundance.
description: Data was collected from a glasshouse experiment conducted at
 University of Pittsburgh in 2019.
description: Metadata for Catella et
 al_NewPhytologist_data.csv is specified in the Catella et
 al_NewPhytologist_ReadMe.doc file.
 Some columns used for analysis were added manually in R
 after data collection, see the main text:
 Geographic origin (native, non-native)
 Competition treatment (plants in the Mono1 and Mono2 trays were
 combined into an 'intra' treatment, and plants in the Mixed
 trays were denoted as the 'inter' treatment)
 Response variables: RII, biomass differences, differential gall
 and nodule density.
DOI: 10.5061/dryad.gf1vhhmqb
title: The role of canopy cover dynamics over a decade of changes in the understory of an Atlantic beech-oak forest

description: This dataset hosts the main data and R codes of the analyses
 carried out to study the role of canopy cover dynamics over a decade of
 changes in the understory of an Atlantic Beech-Oak forest. We measured
 changes in understory taxonomical and functional composition, richness and
 diversity between 2006 and 2016, and relate those changes to changes in
 canopy coverage between both years. The data show changes between 2006 and
 2016 in the species abundance, richness and diversity of 102
 understory communities, and in the functional composition, richness and
 diversity for five functional traits (Leaf dry matter content, Specific
 leaf area, Leaf size, Plant height and Seed mass). Changes in
 canopy coverage between 2006 and 2016 were studied as an explanatory
 variable. The R codes show the main analyses carried out in
 the study: 1) The calculation of the functional composition,
 richness and diversity of the five traits studied (Leaf dry matter
 content, Specific leaf area, Leaf size, Plant height and Seed mass),
 2) a Dunnett’s modified Tukey-Kramer test used to test
 for significant relationships between four plot categories defined
 according to the presence or absence of canopy gaps (no gaps, gap closure,
 gap opening and gap persistence) and changes in the taxonomical and
 functional composition and diversity of the understory from 2006 to 2016.
 3) An Indicator Species Analysis used to study the species that
 were indicators of gap opening or closure in the Atlantic
 Beech-Oak forest studied. 4) The calculation of the Standardized Effect
 Size for the functional traits of the indicator species, used to
 see if the species selected as gap indicators shared similar values of
 functional traits and had values significantly different from
 non-indicator species.
DOI: 10.5061/dryad.nk98sf7tp
title: Data from: Rearing and sampling methods for estimating spruce budworm development rates at constant temperatures

description: We describe an experimental protocol for measuring the response of spruce
 budworm post-diapause larval development to temperature. This protocol is
 specifically designed to include measurements of development near their
 upper and lower thermal thresholds. The application of this protocol to a
 laboratory colony allowed for the first experimental evidence that spruce
 budworm larval development occurs at temperatures as low as 5 ºC and as
 high as 35 ºC and provides data to estimate development rates at
 temperatures from 5–35 ºC in 5 ºC increments. Our protocol is also
 designed to minimize mortality near the thermal development thresholds
 thus allowing for multi-generational studies. We observed developmental
 plasticity in larvae reared at constant temperatures, particularly the
 occurrence of up to 42% of some individuals requiring only five instars to
 complete development, compared to the expected six instars. An occurrence
 that exhibited no clear relation to temperature. While this protocol is
 specifically designed for spruce budworm, it provides a template for the
 study of other species’ developmental responses to temperature.
description: Data collected from rearing of spruce budworm larvae at
 controlled temperatures in a laboratory. Methodological details are
 provided in the associated manuscript and readme file.
description: Data and code are provided to replicate the analysis of head
 capsule widths and the fitting of the Dyer's law relationshop. Data
 and code are also given to reproduce all Figures except 2 &
 5.