cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63c7b
title: Data from: Measuring the success of reforestation for restoring biodiversity and ecosystem functioning

description: Effective assessment of the success of ecological restoration projects is
 critical in justifying the use of restoration in natural resource
 management as well as improving best practice. One of the main goals of
 ecological restoration is the recovery of ecosystem function, yet most
 researchers assume that increasing species and or functional diversity
 equates with restoration of ecosystem function, rather than empirically
 demonstrating these mechanistic relationships. In this study, we assess
 how dung beetle species diversity, community composition, functional
 diversity and ecological functions vary along a restoration chronosequence
 and compare restored areas with reference (rain forest) and degraded
 (pasture) systems. We also directly investigate the dung beetle diversity
 – ecosystem functioning relationship in the context of ecological rain
 forest restoration by testing the predictive power of traditional
 taxonomic indices and functional diversity metrics for functionality.
 Species richness, abundance, biomass and functional richness all increased
 with restoration age, with the oldest restoration sites being most similar
 to rain forest, whereas functional evenness and functional divergence
 decreased with restoration age. Community composition in the restored
 areas was clearly progressing towards the rain forest sites and deviating
 from the pasture sites with increasing restoration age. Secondary seed
 dispersal rates increased with restoration age, but there was only a weak
 positive relationship between dung removal and soil excavation and
 restoration age. Biodiversity metrics explained 47–74% of the variation in
 functions mediated by dung beetles; however, functional trait-based
 indices provided greater explanatory power of functionality than
 traditional species-based metrics. Synthesis and applications. Our results
 provide empirical evidence on the potential of tropical forest restoration
 to mitigate biodiversity losses, recovering not only faunal species
 diversity, but also functional diversity and ecosystem functions in a
 relatively short period of time. We also demonstrate that functional
 trait-based metrics are better predictors of functionality than
 traditional species-based metrics but that the relationship between
 restoration age, diversity and ecosystem functioning is not
 straightforward and depends on the functions, traits and metrics used.
description: Dung beetle community
 and function dataDung beetle community
 and function dataDERHE_ET_AL_BY_SITE_ALL_VARIABLES.xlsx
DOI: 10.5061/dryad.1bt11
title: Data from: Is the pirate really a ghost? Evidence for generalized chemical camouflage in an aquatic predator, Pirate Perch (Aphredoderus sayanus)

description: Camouflage occupies a central role in arsenals of both predators and prey
 and invokes visions of organisms possessing specific characteristics or
 altering their shape, color, or behavior to blend into the visual
 background or confound identification. However, many organisms use
 modalities other than vision. Chemical communication is particularly
 important in aquatic systems, and chemicals cues are used by a broad array
 of colonizing organisms to recognize and avoid risky habitats. Here we
 describe a habitat selection experiment with aquatic beetles and summarize
 results of 11 experiments involving colonizing beetles and ovipositing
 tree frogs that provide evidence that pirate perch Aphredoderus sayanus
 are chemically camouflaged with respect to a diverse array of prey
 organisms. We believe this to be the first example of a predator
 possessing a generalized chemical camouflage effective against a broad
 array of prey organisms, and we suggest that it may constitute a novel
 weapon in the predator-prey arms race.
description: Summaryofdata for
 Cloaking (version 1)summary from published
 data and several unpublished experiments.
DOI: 10.5061/dryad.gk110
title: Data from: HIV dynamics linked to memory CD4+ T cell homeostasis

description: The dynamics of latent HIV is linked to infection and clearance of resting
 memory CD4+ T cells. Infection also resides within activated, non-dividing
 memory cells and can be impacted by antigen-driven and homeostatic
 proliferation despite suppressive antiretroviral therapy (ART). We
 investigated whether plasma viral level (pVL) and HIV DNA dynamics could
 be explained by HIV’s impact on memory CD4+ T cell homeostasis. Median
 total, 2-LTR and integrated HIV DNA levels per μL of peripheral blood, for
 8 primary (PHI) and 8 chronic HIV infected (CHI) individuals enrolled on a
 raltegravir (RAL) based regimen, exhibited greatest changes over the 1st
 year of ART. Dynamics slowed over the following 2 years so that total HIV
 DNA levels were equivalent to reported values for individuals after 10
 years of ART. The mathematical model reproduced the multiphasic dynamics
 of pVL, and levels of total, 2-LTR and integrated HIV DNA in both PHI and
 CHI over 3 years of ART. Under these simulations, residual viremia
 originated from reactivated latently infected cells where most of these
 cells arose from clonal expansion within the resting phenotype. Since
 virion production from clonally expanded cells will not be affected by
 antiretroviral drugs, simulations of ART intensification had little impact
 on pVL. HIV DNA decay over the first year of ART followed the loss of
 activated memory cells (120 day half-life) while the 5.9 year half-life of
 total HIV DNA after this point mirrored the slower decay of resting memory
 cells. Simulations had difficulty reproducing the fast early HIV DNA
 dynamics, including 2-LTR levels peaking at week 12, and the later slow
 loss of total and 2-LTR HIV DNA, suggesting some ongoing infection. In
 summary, our modelling indicates that much of the dynamical behavior of
 HIV can be explained by its impact on memory CD4+ T cell homeostasis.
description: HIV data for primary
 (PHI) and chonic (CHI) HIV infected groupsPHICHI_means_dryad.xlsx
DOI: 10.5061/dryad.1fp259b
title: Data from: Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA

description: Understanding factors that influence observation processes is critical for
 accurate assessment of underlying ecological processes. When indirect
 methods of detection, such as environmental DNA, are used to determine
 species presence, additional levels of uncertainty from observation
 processes need to be accounted for. We conducted a field trial to evaluate
 observation processes of a terrestrial invasive species (wild pigs- Sus
 scrofa) from DNA in water bodies. We used a multi-scale occupancy analysis
 to estimate different levels of observation processes (detection, p): the
 probability DNA is available per sample (θ), the probability of capturing
 DNA per extraction (γ), and the probability of amplification per qPCR run
 (δ). We selected four sites for each of three water body types and
 collected 10 samples per water body during two months (September and
 October 2016) in central Texas. Our methodology can be used to guide
 sampling adaptively to minimize costs while improving inference of species
 distributions. Using a removal sampling approach was more efficient than
 pooling samples, and was unbiased. Availability of DNA varied by month,
 was considerably higher when water pH was near neutral, and was higher in
 ephemeral streams relative to wildlife guzzlers and ponds. To achieve a
 cumulative detection probability greater than 90% (including availability,
 capture, and amplification), future studies should collect 20 water
 samples per site, conduct at least 2 extractions per sample, and conduct 5
 qPCR replicates per extraction. Accounting for multiple levels of
 uncertainty of observation processes improved estimation of the ecological
 processes and provided guidance for future sampling designs.
description: eDNA Data by month and
 water bodySamples are provided by
 month and water body with corresponding covariate information (water body
 type, pH, water sample depth, days since last pig visit, number of
 pictures of pigs per month, and average pig group size). The qPCR results
 are shown (simplified to zeros and ones that were used in this analysis).
 The first six columns of the qPCR results are from the pooled sample data
 (first 3 are pre-inhibitor removal, next 3 are post-inhibitor removal).
 The next 40 columns are the qPCR results by sample (first 20 are
 pre-inhibitor removal, next 20 are post-inhibitor
 removal).eDNAData.xlsx
DOI: 10.5061/dryad.bj3570d
title: Data from: Micro/nano-hierarchical structured TiO2 coating on titanium by micro-arc oxidation enhances osteoblast adhesion and differentiation

description: Nano-structured and micro/nano-hierarchical structured TiO2 coatings were
 produced on polished titanium by the micro-arc oxidation (MAO) technique.
 This study was conducted to screen a suitable structured TiO2 coating for
 osteoblast adhesion and differentiation in dental implants. The
 formulation was characterized by scanning electron microscopy (SEM), X-ray
 diffraction (XRD), and wettability testing. Adhesion, proliferation, and
 osteogenic differentiation of MG63 cells were analysed by SEM, Cell
 Counting Kit-8 (CCK-8), and quantitative real-time PCR. The
 micro/nano-hierarchical structured TiO2 coating with both slots and pores
 showed the best morphology and wettability. XRD analysis revealed that
 rutile predominated along with a minor amount of anatase in both TiO2
 coatings. Adhesion and extension of MG63 cells on the
 micro/nano-hierarchical structured TiO2 coating were the most favourable.
 MG63 cells showed higher growth rates on the micro/nano-hierarchical
 structured TiO2 coating at 1 and 3 days. Osteogenic-related gene
 expression was markedly increased in the micro/nano-hierarchical
 structured TiO2 coating group compared to in the polished titanium group
 at 7, 14, and 21 days. These results revealed the micro/nano-hierarchical
 structured TiO2 coating as a promising surface modification and suitable
 biomaterial for use with dental implants.
description: Raw
 dataThis file contains raw
 data of contact angle assay(figure 3)， cell proliferation assay(figure
 5)，and quantitative real-time PCR(figure 6).
DOI: 10.5061/dryad.89d3q90
title: Data from: Avoided emissions and conservation of scrub mangroves: a potential Blue Carbon project in the Gulf of California, Mexico

description: Mangroves are considered ideal ecosystems for Blue Carbon projects.
 However, because of their short stature, some mangroves (“scrub”
 mangroves, &lt; 2m) do not fulfil the current definition of “forests”
 which makes them ineligible for emission reduction programs such as REDD+.
 Short stature mangroves can be the dominant form of mangroves in arid and
 poor nutrient landscapes, and emissions from their deforestation and
 degradation could be substantial. Here, we describe a potential Blue
 Carbon project in the Gulf of California, Mexico, to illustrate that
 projects which avoid emissions from deforestation and degradation could
 provide financial resources to protect mangroves that cannot be included
 in other emission reduction programs. The goal of the project is to
 protect 16,058 ha of mangroves through conservation concessions from the
 Mexican Federal Government. The cumulative avoided emissions of the
 project are 2.84 million Mg CO2 over 100 years, valued at $US 426,000 per
 year (US$15 per Mg CO2 in the California market). The funds could be used
 for community-based projects that will improve mangrove management, such
 as surveillance, eradication of invasive species, rehabilitation after
 tropical storms, and environmental education. The strong institutional
 support, secure financial status, community engagement, and clear project
 boundaries provide favourable conditions to implement this Blue Carbon
 project. Financial resources from Blue Carbon projects, even in mangroves
 of short stature, can provide substantial resources to enhance community
 resilience and mangrove protection.
description: Data C stocks_Gulf
 California_Carbon stocks from
 mangrove forest in the Gulf of California (Baja California Sur, Sinaloa,
 Sonora), Mexico. Carbon stocks include trees (aboveground and roots) and
 soil stocks to 1m in depth.
DOI: 10.5061/dryad.k50s6
title: Data from: Low intensity blood parasite infections do not reduce the aerobic performance of migratory birds

description: Blood parasites (Haemosporidia) are thought to impair the flight
 performance of infected animals, and therefore, infected birds are
 expected to differ from their non-infected counterparts in migratory
 capacity. Since haemosporidians invade host erythrocytes, it is commonly
 assumed that infected individuals will have compromised aerobic capacity,
 but this has not been examined in free-living birds. We tested if
 haemosporidian infections affect aerobic performance by examining
 metabolic rates and exercise endurance in migratory great reed warblers
 (Acrocephalus arundinaceus) experimentally treated with Plasmodium
 relictum pGRW04 and in naturally infected wild birds over consecutive life
 history stages. We found no effect of acute or chronic infections on
 resting metabolic rate, maximum metabolic rate or exercise endurance in
 either experimentally treated or free-living birds. Oxygen consumption
 rates during rest and while undergoing maximum exercise as well as
 exercise endurance increased from breeding to migration stages in both
 infected and non-infected birds. Importantly, phenotypic changes
 associated with preparation for migration were similarly unaffected by
 parasitaemia. Consequently, migratory birds experiencing parasitaemia
 levels typical of chronic infection do not differ in migratory capacity
 from their uninfected counterparts. Thus, if infected hosts differ from
 uninfected conspecifics in migration phenology, another mechanism than
 changes in aerobic capacity should be involved.
description: Data for
 LowParasitemia_AerobicPerformance In MigratoyBirdsThe file contains all
 data for displaying the figures (incl. supplement). For raw data on
 respirometry, please contact:
 steffen.hahn@vogelwarte.chHahn_etal_Low
 ParasitemiaAerobicPerformanceMigratoyBirds_data.xlsx
DOI: 10.5061/dryad.rd2s3
title: Data from: Likelihood inference of non-constant diversification rates with incomplete taxon sampling

description: Large-scale phylogenies provide a valuable source to study background
 diversification rates and investigate if the rates have changed over time.
 Unfortunately most large-scale, dated phylogenies are sparsely sampled
 (fewer than 5% of the described species) and taxon sampling is not
 uniform. Instead, taxa are frequently sampled to obtain at least one
 representative per subgroup (e.g. family) and thus to maximize diversity
 (diversified sampling). So far, such complications have been ignored,
 potentially biasing the conclusions that have been reached. In this study
 I derive the likelihood of a birth-death process with non-constant
 (time-dependent) diversification rates and diversified taxon sampling.
 Using simulations I test if the true parameters and the sampling method
 can be recovered when the trees are small or medium sized (fewer than 200
 taxa). The results show that the diversification rates can be inferred and
 the estimates are unbiased for large trees but are biased for small trees
 (fewer than 50 taxa). Furthermore, model selection by means of
 Akaike's Information Criterion favors the true model if the true
 rates differ sufficiently from alternative models (e.g. the birth-death
 model is recovered if the extinction rate is large and compared to a
 pure-birth model). Finally, I applied six different diversification rate
 models – ranging from a constant-rate pure birth process to a decreasing
 speciation rate birth-death process but excluding any rate shift models –
 on three large-scale empirical phylogenies (ants, mammals and snakes with
 respectively 149, 164 and 41 sampled species). All three phylogenies were
 constructed by diversified taxon sampling, as stated by the authors.
 However only the snake phylogeny supported diversified taxon sampling.
 Moreover, a parametric bootstrap test revealed that none of the tested
 models provided a good fit to the observed data. The model assumptions,
 such as homogeneous rates across species or no rate shifts, appear to be
 violated.
description: Analysis_AntsThe R script to perform the diversification rate analysis of the ant phylogeny under diversified taxon sampling and uniform taxon sampling.Analysis_MammaliaThe R script performing the diversification rate analysis of the mammal phylogeny under diversified taxon sampling and uniform taxon sampling.Analysis_SnakesThe R script performing the diversification rate analysis of the snake phylogeny under diversified taxon sampling and uniform taxon sampling.AntsAnt phylogeny of Moreau CS, Bell CD, Vila R, Archibald SB, Pierce NE (2006) Phylogeny of the ants: diversi cation in the age of angiosperms. Science 312: 101-104.MammaliaThe mammal phylogeny of Meredith R, Jane cka J, Gatesy J, Ryder O, Fisher C, et al. (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversi cation. Science 334: 521-524.SnakesThe snake phylogeny of Pyron RA, Burbrink FT (2012) Extinction, ecological opportunity, and the origins of global snake diversity. Evolution 66: 163-178.
DOI: 10.5061/dryad.bd7q6
title: Data from: Evidence of reduced individual heterogeneity in adult survival of long-lived species

description: The canalization hypothesis postulates that the rate at which trait
 variation generates variation in the average individual fitness in a
 population determines how buffered traits are against environmental and
 genetic factors. The ranking of a species on the slow-fast continuum – the
 covariation among life-history traits describing species-specific life
 cycles along a gradient going from a long life, slow maturity, and low
 annual reproductive output, to a short life, fast maturity, and high
 annual reproductive output – strongly correlates with the relative fitness
 impact of a given amount of variation in adult survival. Under the
 canalization hypothesis, long-lived species are thus expected to display
 less individual heterogeneity in survival at the onset of adulthood, when
 reproductive values peak, than short-lived species. We tested this
 life-history prediction by analysing long-term time series of
 individual-based data in nine species of birds and mammals using
 capture-recapture models. We found that individual heterogeneity in
 survival was higher in species with short-generation time (&lt; 3
 years) than in species with long generation time (&gt; 4 years). Our
 findings provide the first piece of empirical evidence for the
 canalization hypothesis at the individual level from the wild.
description: Raw
 dataRaw outputs of CMR
 models for our 11 study species, with variance and covariance. Column
 headings are annotated with legend.
DOI: 10.5061/dryad.kv206p0
title: Data from: Age and performance at fledging is a cause and consequence of juvenile mortality between life stages

description: Should they stay or should they leave? The age at which young transition
 between life stages, such as living in a nest versus leaving it, differs
 among species and the reasons why are unclear. We show that offspring of
 songbird species that leave the nest at a younger age have less-developed
 wings that cause poorer flight performance and greater mortality after
 fledging. Experimentally delayed fledging verified that older age and
 better developed wings provide benefits of reduced juvenile mortality.
 Young are differentially constrained in the age that they can stay in the
 nest and enjoy these fitness benefits because of differences among species
 in opposing predation costs while in the nest. This tension between
 mortality in versus outside of the nest influences offspring traits and
 performance and creates an unrecognized conflict between parents and
 offspring that determines the optimal age to fledge.
description: Juvenile mortality
 performance data
DOI: 10.5061/dryad.9fs476vt
title: Data from: Evolution of pre-mating reproductive isolation among conspecific populations of the sea rock-pool beetle Ochthebius urbanelliae driven by reinforcing natural selection

description: How natural selection might be involved in speciation remains a
 fundamental question in evolutionary biology. When two or more species
 co-occur in the same areas, natural selection may favour divergence in
 mating traits. By acting in sympatric but not allopatric populations,
 natural selection can also affect mate choice within species and
 ultimately initiate speciation among conspecific populations. Here we
 address this potential effect in the sea rock-pool beetles Ochthebius
 quadricollis and O.urbanelliae. The two species, which inhabit the
 Mediterranean coasts, co-occurr syntopically in an area along the Italian
 Tyrrhenian coast and completed reproductive isolation by reinforcement. In
 this paper, through mating trials under laboratory conditions between
 conspecific populations, we found in O.quadricollis no deviations from
 random mating. Conversely, in O.urbanelliae, we found a clear pattern of
 pre-mating isolation between the reinforced populations sympatric with
 O.quadricollis and those non-reinforced allopatric. This pattern is
 consistent with the view that natural selection, which completed the
 reproductive isolation between the two species in sympatry, led
 incidentally also to partial pre-mating reproductive isolation (IPSI
 estimator from 0.683 to 0.792) between conspecific populations of
 O.urbanelliae. This case study supports an until recently underappreciated
 role of natural selection resulting from species interactions in
 initiating speciation.
description: Marking
 testsMarking tests: Number of
 beetles that had lost their paint mark and number of dead beetles in
 marking tests using yellow and white Polycolor paint; Number of couples
 collected in marking tests using yellow and white Polycolor paint; Number
 of discarded couples collected in the multiple-choice mating trials for
 Ochthebius quadricollis and O. urbanelliae.
DOI: 10.5061/dryad.1nn7v
title: Data from: Gene transcription in sea otters (Enhydra lutris): development of a diagnostic tool for sea otter and ecosystem health

description: Gene transcription analysis for diagnosing or monitoring wildlife health
 requires the ability to distinguish pathophysiological change from natural
 variation. Herein we describe methodology for the development of
 quantitative real time polymerase chain reaction (qPCR) assays to measure
 differential transcript levels of multiple immune-function genes in the
 sea otter (Enhydra lutris); sea otter specific, qPCR primer sequences for
 the genes of interest are defined. We establish a “reference” range of
 transcripts for each gene in a group of clinically healthy captive and
 free-ranging sea otters. The 10 genes of interest represent multiple
 physiological systems that play a role in immuno-modulation, inflammation,
 cell protection, tumor suppression, cellular stress-response, xenobiotic
 metabolizing enzymes, antioxidant enzymes, and cell-cell adhesion. The
 cycle threshold (CT) measures for most genes were normally distributed;
 the complement cytolysis inhibitor was the exception. The relative
 enumeration of multiple gene transcripts in simple peripheral blood
 samples expands the diagnostic capability currently available to assess
 the health of sea otters in situ and provides a better understanding of
 the state of their environment.
description: Figure 1 and Table 4
 71811