cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.95rf4
title: Data from: Balancing yield with resilience and conservation objectives in harvested predator-prey communities

description: The global overexploitation of fish stocks is endangering many marine food
 webs. Scientists and managers now call for an ecosystem-based fisheries
 management, able to take into account the complexity of marine ecosystems
 and the multiple ecosystem services they provide. By contrast, many
 fishery management plans only focus on maximizing the productivity of
 harvested stocks. Such practices are suggested to affect other ecosystem
 services, altering the integrity and resilience of natural communities.
 Here we show that while yield-maximizing policies can allow for
 coexistence and resilience in predator-prey communities, they are not
 optimal in a multi-objective context. We find that although total prey and
 predator maximum yields are higher with a prey-oriented harvest, focusing
 on the predator improves species coexistence. Also, moderate harvesting of
 the predator can enhance resilience. Furthermore, increasing maximum
 yields by changing catchabilities improves resilience in predator-oriented
 systems, but reduces it in prey-oriented systems. In a multi-objective
 context, optimal harvesting strategies involve a general trade-off between
 yield and resilience. Resilience-maximizing strategies are however
 compatible with quite high yields, and should often be favored. Our
 results further suggest that balancing harvest between trophic levels is
 often best at maintaining simultaneously species coexistence, resilience
 and yield.
description: fig1_fig2Scilab script used to plot Figures 1 and 2fig3Scilab script used to plot Figure 3fig4Scilab script used to plot Figure 4fig5Scilab script used to plot Figure 5
DOI: 10.5061/dryad.6r40g
title: Data from: Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkey

description: Immunogenetic data from wild primate populations have been difficult to
 obtain, due to logistic and methodological constraints. We applied a
 well-characterized deep sequencing method for MHC I typing, developed for
 macaques, to a population of wild red colobus to assess the feasibility of
 identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data
 from blood and tissue samples to assign haplotypes. Eighty-two sequences
 were classified as red colobus MHC I alleles distributed across six MHC I
 loci. Individuals averaged ~13 k reads across six MHC I loci, with 83 % of
 all alleles representing either MHC I-A or MHC I-B loci. This study not
 only represents an important advance in the identification and genotyping
 of MHC in the endangered red colobus but also shows the potential for
 using this approach in other endangered wild primates.
description: RedColobus_MHCI_fastaRedColobus_MHCI.fa
DOI: 10.5061/dryad.12r74m2
title: Data from: Climate structuring of Batrachochytrium dendrobatidis infection in the threatened amphibians of the northern Western Ghats, India

description: Batrachochytrium dendrobatidis (Bd) is a pathogen killing amphibians
 worldwide. Its impact across much of Asia is poorly characterised. This
 study systematically surveyed amphibians for Bd across rocky plateaus in
 the northern section of the Western Ghats Biodiversity Hotspot, India,
 including for the first surveys of the plateaus in the coastal region.
 These ecosystems offer an epidemiological model system since they are
 characterised by differing levels of connectivity, edaphic and climatic
 conditions, and anthropogenic stressors. One hundred and eighteen
 individuals of 21 species of Anura and Apoda on 13 plateaus ranging from
 67-1179m above sea level and 15.89 to 17.92° North Latitude were sampled.
 Using qPCR protocols 79% of species and 27% of individuals tested were
 positive for Bd. This is the first record of Bd in caecilians in India,
 the Critically Endangered Xanthophryne tigenrinus and Endangered
 Fejervarya cf. sahyadris. Mean site prevalence was 28.15%. Prevalence
 below the escarpment was 31.2% and 25.4% above. The intensity of infection
 (GE) showed the reverse pattern. Infection may be related to elevational
 temperature changes, thermal exclusion, inter-site connectivity and
 anthropogenic disturbance. Coastal plateaus may be thermal refuges from
 Bd. Infected amphibians represented a wide range of ecological traits
 posing interesting questions about transmission routes.
description: Thorpe et al. 2018.
 Chytrid possitives from the Western Ghats. GE Distribution
 TableTabulated positive
 results for amphibians infected with the pathogenic fungus
 Batrachochytrium dendrobatidis found in the northern Western Ghats, south
 west India. Amphibian samples from species complexes that are poorly
 resolved are shown as 'cf' as molecular confirmation of identity
 was not available at the time of upload.
DOI: 10.5061/dryad.nn27f
title: Data from: Is sex advantageous in adverse environments? A test of the abandon-ship hypothesis

description: Understanding the evolution and maintenance of sexual reproduction remains
 a long-standing challenge in evolutionary biology. Stress often induces
 sexual reproduction in facultatively sexual species (those species capable
 of both sexual and asexual reproduction). The abandon-ship hypothesis
 predicts higher allocation to sex under stress to allow low-fitness
 individuals to recombine their genotype, potentially increasing offspring
 fitness. However, effective tests of the abandon-ship hypothesis,
 particularly in multicellular organisms, are lacking. Here we test the
 abandon-ship hypothesis, using cyanogenic and acyanogenic defense
 phenotypes of the short-lived perennial herb Trifolium repens.
 Cyanogenesis provides an effective defense against herbivores and is under
 relatively simple genetic control (plants dominant for cyanogenesis at two
 alleles express the defended phenotype). Thus, maladapted individuals can
 acquire adaptive defense alleles for their offspring in a single episode
 of sexual reproduction. Plants were grown under high- and low-herbivory
 treatments (plants were exposed to herbivorous snails) and a control
 treatment (no herbivory). Herbivores reduced growth and fitness in all
 treated plants, but herbivory induced higher sexual allocation only in
 maladapted (acyanogenic) individuals. Overall, our results support the
 abandon-ship hypothesis.
description: griffiths and bonser
 dataData collected from
 glasshouse experiment. Two defense genotypes (cyanogenic and acyanogenic)
 and three herbivory treatments (High, Low, and No). Methods for
 calculating sexual and clonal reproductive effort are described in the
 paper.
DOI: 10.5061/dryad.3h7q736
title: Data from: Allocation strategies for nitrogen and phosphorus in forest plants

description: The allocation of limiting elements, such as nitrogen (N) and phosphorus
 (P), in plants is an important basis for structural stability and
 functional optimization in natural plant communities. However, because of
 the lack of systematic investigation data, the mechanisms of optimal
 nutrient allocation in plants in natural forests are still unclear. Using
 consistent measurements of N and P contents in 930 plant species, we
 explored the allocation strategies for N and P in different plant organs
 and plant functional groups (PFGs) in natural communities. The N and P
 contents and N:P ratio were the highest in the leaf (the most active
 organ) at the organ level. At the PFG level, the N and P contents were
 higher in herbs than in woody plants, but the trend was opposite for the
 N:P ratio. The elemental plasticity of root was higher than that of leaf.
 Furthermore, at the large scale, the allometric exponents of N and P were
 less than 1 and showed no difference, indicating strong conservatism of
 the scaling relationship in plants. In summary, higher element content in
 more active organs, higher element plasticity in underground organs, and
 conservative allometric allocation among different organs and among
 different PFGs jointly constitute the optimal strategies for the
 allocation of limiting elements.
description: nitrogen and phosphorus
 conteens and N:P of different organs of different plant functional organs
 in forestsOIK-05517.R1-Dryad
 file.xlsx
DOI: 10.5281/zenodo.18385198
title: SEM Withered Plant (BSE Series) — Kikoh Matsuura (Art–Science Archive)

description: Parent (series) record for *SEM Withered Plant (BSE)* by Kikoh Matsuura.  This record serves as the hub for all child datasets in the series.

**Files included:**- A series overview (TXT) documenting scope, naming rules, citation style, and file policy- A machine-readable index (CSV) that will be updated to list child datasets (DOIs, imaging parameters, etc.)- Withered Plant — Declaration (PDF) — issued once / no future revisions / no images- Withered Plant: Phase I (DOI 1–100) — Record (PDF) — fixed record / no future revisions

Each child dataset contains raw, uncompressed BMP images (≈10 per set, number varies) acquired with a personally owned TECHNEX TinySEM M3-i using the BSE detector under high-vacuum conditions.  Child records provide detailed READMEs with exact parameters (accelerating voltage, working distance, vacuum, pixel size, field of view, frame time, coating).

This parent provides a stable concept DOI for the entire *SEM Withered Plant (BSE)* series.  Child datasets link back via *IsPartOf*, and this parent enumerates them via *HasPart*.  

*This series visualizes the hidden order and chance in withered plants through SEM-BSE, leaving a unique trace at the boundary between art and science.*
DOI: 10.5061/dryad.1t75d
title: Data from: Functional dissimilarity, not phylogenetic relatedness, determines interspecific interactions among plants in the Tibetan alpine meadows

description: The hypotheses suggesting that the nature and strength of species
 interactions should be determined by phylogenetic relatedness have
 important implications for the understanding of community structure.
 However, to date, there is limited empirical evidence to support them. At
 least two basic conditions need to be met in order to expect species
 interactions to be determined by evolutionary relatedness: a phylogenetic
 signal in the traits involved in the interactions and changes in the
 interactions as species are more ecologically similar. Here, we report
 results of a removal experiment in the Chinese Tibetan plateau in which we
 directly assessed if the nature and/or strength of interactions among
 twelve alpine meadow plant species were influenced by their phylogenetic
 relatedness and/or their functional dissimilarity. For each plant species,
 we compared its biomass production when grown alone to its biomass in
 presence of another species and used it as a measure of species
 interactions. Competition between pairs of species was more frequent than
 facilitation, with 60% of interactions resulting in plants producing less
 biomass when a second species was present. We found no effect of
 phylogenetic relatedness on the prevalence or intensity of competition or
 facilitation, presumably as none of the studied traits showed phylogenetic
 signal. Functional dissimilarity based on maximum plant height alone was
 the best predictor of both the prevalence and strength of competition and
 facilitation, followed by functional dissimilarity using all five
 functional traits. Our results pinpoint the limited capacity of
 phylogenetic relatedness as predictor of species interactions; underlining
 the limitations of using phylogenetic dispersion patterns to infer
 mechanisms of community assembly. On the contrary, when the right
 functional traits are used, functional dissimilarity among species can
 predict both the nature and strength of their interactions; accentuating
 the relevance of trait-based approaches in community ecology research.
description: PD, FD and
 RIIPhyogenetic diversity
 (PD), six functional diversity (FD) indices and relative interaction
 intensity (RII) used in the paper. The data inclded all 144
 subplots.
DOI: 10.5061/dryad.89qf8
title: Data from: Towards improving searches for optimal phylogenies

description: Finding the optimal evolutionary history for a set of taxa is a
 challenging computational problem, even when restricting possible
 solutions to be “tree-like” and focusing on the maximum-parsimony
 optimality criterion. This has led to much work on using heuristic tree
 searches to find approximate solutions. We present an approach for finding
 exact optimal solutions that employs and complements the current heuristic
 methods for finding optimal trees. Given a set of taxa and a set of
 aligned sequences of characters, there may be subsets of characters that
 are compatible, and for each such subset there is an associated (possibly
 partially resolved) phylogeny with edges corresponding to each character
 state change. These perfect phylogenies serve as anchor trees for our
 constrained search space. We show that, for sequences with compatible
 sites, the parsimony score of any tree T is at least the parsimony score
 of the anchor trees plus the number of inferred changes between T and the
 anchor trees. As the maximum-parsimony optimality score is additive, the
 sum of the lower bounds on compatible character partitions provides a
 lower bound on the complete alignment of characters. This yields a region
 in the space of trees within which the best tree is guaranteed to be
 found; limiting the search for the optimal tree to this region can
 significantly reduce the number of trees that must be examined in a search
 of the space of trees. We analyze this method empirically using four
 different biological data sets as well as surveying 400 data sets from the
 TreeBASE repository, demonstrating the effectiveness of our technique in
 reducing the number of steps in exact heuristic searches for trees under
 the maximum-parsimony optimality criterion.
description: scriptThis is a Python script,
 along with two dependencies, another Python script, and a Perl script. The
 main script uses consecutive POY searches to discover anchor trees. Usage
 instructions are included in the comments at the beginning of the
 script.
DOI: 10.15468/dl.59wrr9
title: Occurrence Download

description: A dataset containing 985 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neoaliturus fenestratus"
 ]
}

 The dataset includes 985 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001361-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n2q50
title: Data from: Quantifying risk of overharvest when implementation is uncertain

description: 1. Sustainable harvest management implies an ability to control harvest
 rates. This is challenging in systems that have limited control of
 resources and resource users, which is often the case in small game
 harvest management. The difference between management strategies and
 actual harvest bag size (i.e. implementation uncertainty) may be
 substantial, but few studies have explored this. 2. We investigated how
 different management strategies and ecosystem variables affected realised
 harvest of willow ptarmigan (Lagopus lagopus L.) among nine
 independently-managed, state-owned hunting areas in Central and South
 Norway during 2008-2015. First, we focused our empirical analysis around
 three response variables of interest: hunting bag (scaled by area),
 hunting effort (number of hunting days scaled by area) and hunter
 efficiency (shot birds per hunting day). Akaike’s Information Criteria
 (AIC) guided model selection among candidate GLMMs. Then, we used
 model-averaged parameter estimating from the statistical models in
 numerical simulations to explore risk of overharvest due to implementation
 uncertainty. 3. The most parsimonious model explaining hunting bag
 included total allowable catch (TAC) and willow ptarmigan density. Hunting
 effort was explained by number of permits sold and type of quota (daily
 vs. weekly quota). The most parsimonious model describing hunter
 efficiency only included the effect of willow ptarmigan density. 4. Our
 results show that managers have only partial control over harvest rates in
 this system, and that hunters were relatively more efficient and harvest
 rates higher at low densities. This effect was present for all management
 strategy scenarios, including when managers adjusted TAC according to
 population estimates from monitoring programs. 5. Synthesis and
 applications. Quantifying risk of unsustainable harvest rates under
 different scenarios enables managers to make informed decisions, when
 dealing with competing objectives of harvest opportunities and
 sustainability. The substantial risk of high harvest rates at low
 densities reported here should encourage frequent use of threshold
 strategies. This study is one of the first approaches for quantifying
 implementation uncertainty in small game harvest, and shows how estimates
 from empirical analyses could be used to quantify risk of overharvest.
description: Eriksen, Moa &
 Nilsen: Ptarmigan management dataData used for empirical
 analyses. Contains data on willow ptarmigan harvest, management strategies
 and ecosystem characteristics.Eriksen_Moa_Nilsen_Ptarmigan_management_data.csvEriksen, Moa & Nilsen: Harvest simulationsR-script used for simulating harvest within different management strategies, at a range of densities, under uncertain implementation. Two alternative model paths are presented.Eriksen_Moa_Nilsen_Harvest_simulations.R
DOI: 10.5061/dryad.j76q1
title: Data from: Matrilineal inheritance of a key mediator of prenatal maternal effects

description: Sex-linkage is predicted to evolve in response to sex-specific or sexually
 antagonistic selection. In line with this prediction, most sex-linked
 genes are associated with reproduction in the respective sex. In addition
 to traits directly involved in fertility and fecundity, mediators of
 maternal effects may be predisposed to evolve sex-linkage, because they
 indirectly affect female fitness through their effect on offspring
 phenotype. Here, we test for sex-linked inheritance of a key mediator of
 prenatal maternal effects in oviparous species, the transfer of maternally
 derived testosterone to the eggs. Consistent with maternal inheritance, we
 found that in Japanese quail (Coturnix japonica) granddaughters resemble
 their maternal (but not their paternal) grandmother in yolk testosterone
 deposition. This pattern of resemblance was not due to non-genetic priming
 effects of testosterone exposure during prenatal development, as an
 experimental manipulation of yolk testosterone levels did not affect the
 females' testosterone transfer to their own eggs later in life.
 Instead, W chromosome and/or mitochondrial variation may underlie the
 observed matrilineal inheritance pattern. Ultimately, the inheritance of
 mediators of maternal effects along the maternal line will allow for a
 fast and direct response to female-specific selection, thereby affecting
 the dynamics of evolutionary processes mediated by maternal effects.
description: Yolk T
 inheritanceYolk testosterone
 concentrations (pg/mg yolk) in the eggs of Japanese quail across three
 generations (daughters, mothers, maternal grandmothers, paternal
 grandmothers).Priming effects of yolk
 TEffects of a yolk
 testosterone manipulaiton on the yolk T deposition (pg / mg yolk) of
 females that developed in the manipulated eggs, and their
 daughters.
DOI: 10.5061/dryad.9j7fd75
title: Data from: Male harassment, female movements, and genetic diversity in a fragmented metapopulation

description: Interactions with males often alter the short‐term behaviors of
 reproductive females. Yet, the influence of different internal and
 external factors, such as sexual conflict, on animal movement and patch
 dynamics is not well understood. We studied associations between
 courtship, movements of reproductive females, and genetic diversity in a
 small, fragmented network of Euphydras editha taylori (Taylor's
 checkerspot butterfly). In the absence of courtship, female movements
 (step lengths) were restricted (&lt; 2 m) and tortuous, and females
 never departed reproductive habitat. However, when courted by males, step
 lengths increased markedly and movements were straighter (less tortuous).
 Female habitat departures were associated with interactions between patch
 identity and courtship. All tracked females remained in reproductive
 habitat in the smallest patch, whereas 32% of females departed the larger
 patch (over forest) while eluding courting males. Genotyping (simple
 sequence repeats ‐ SSRs) suggested low levels of genetic differentiation
 (Fst ~ 0.02; Analysis of molecular variance p = 0.02) with inter‐patch
 distances of ≤ 0.3 km. Tests for a recent genetic bottleneck were
 negative, but heterozygous deficient deviations from Hardy‐Weinberg
 Equilibrium expectations may indicate a developing bottleneck.
 Patch‐specific female movement behaviors and the distribution of SSR
 alleles across the network suggest the possibility of a predominantly
 unidirectional transfer of reproducing females from the largest to smaller
 patches, with the smaller patches mostly closed to emigration. Our study
 suggests short‐lived intraspecific interactions may influence dispersal in
 unanticipated ways and that understanding these interactions will provide
 a more holistic view of habitat fragmentation and network functioning.
description: Severns and Breed
 Ecography SSR dataThese are SSR fragment
 lengths from genotyping post-diapause larvae collected from three
 different sized patches (small, medium, large) in Euphydryas editha
 taylori patches in western Oregon USA.Severns and Breed Ecography for
 Dryad.xlsx
DOI: 10.5061/dryad.dk3q0
title: Data from: Th2 cytokines inhibit lymphangiogenesis

description: Lymphangiogenesis is the process by which new lymphatic vessels grow in
 response to pathologic stimuli such as wound healing, inflammation, and
 tumor metastasis. It is well-recognized that growth factors and cytokines
 regulate lymphangiogenesis by promoting or inhibiting lymphatic
 endothelial cell (LEC) proliferation, migration and differentiation. Our
 group has shown that the expression of T-helper 2 (Th2) cytokines is
 markedly increased in lymphedema, and that these cytokines inhibit
 lymphatic function by increasing fibrosis and promoting changes in the
 extracellular matrix. However, while the evidence supporting a role for T
 cells and Th2 cytokines as negative regulators of lymphatic function is
 clear, the direct effects of Th2 cytokines on isolated LECs remains poorly
 understood. Using in vitro and in vivo studies, we show that physiologic
 doses of interleukin-4 (IL-4) and interleukin-13 (IL-13) have profound
 anti-lymphangiogenic effects and potently impair LEC survival,
 proliferation, migration, and tubule formation. Inhibition of these
 cytokines with targeted monoclonal antibodies in the cornea suture model
 specifically increases inflammatory lymphangiogenesis without concomitant
 changes in angiogenesis. These findings suggest that manipulation of
 anti-lymphangiogenic pathways may represent a novel and potent means of
 improving lymphangiogenesis.
description: Raw
 DataRaw
 data