cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.231m570
title: Data from: Species characteristics affect local extinctions

description: Premise of the study. Human activities threaten thousands of species with
 extinction. However, it remains difficult to predict extinction risk for
 many vulnerable species. Species characteristics help predict responses to
 anthropogenic environmental change and may help predict likelihood of
 extinction. Phylogenetic signatures of extinction can also provide
 insights into patterns of species loss. Historical data on species losses
 can allow for testing phylogenetic patterns in extinctions and identifying
 traits that influence species vulnerability to local extinction both
 within particularly threatened habitat types and across habitats. Methods.
 We use historical botanical data from Kalamazoo County, Michigan, USA, to
 examine whether species characteristics (community association, native
 status, growth form, life history, range edge, habitat specialization,
 N-fixation, photosynthetic pathway, and rarity) or phylogenetic
 relatedness explain local species loss at the county level. Key results.
 Across Kalamazoo County, prairie species, species at the edge of their
 native range, regionally rare species, and habitat specialists were most
 likely to become locally extinct. Prairie species experienced the highest
 local extinction rates of any habitat type, and among prairie species,
 regionally rare and specialist species were most vulnerable to loss. We
 found no phylogenetic pattern in plant extinctions. Conclusions. Rare,
 habitat specialist species occupying particularly threatened habitats are
 most at risk of local extinction. Given that neither phylogenetic patterns
 nor other characteristics that commonly predict responses to global change
 predicted extinction in our dataset, identifying mechanisms to conserve
 rare or declining species and preventing further habitat destruction may
 be the most effective strategies for reducing future extinction. If you
 would like your personal information to be removed from the database,
 please contact the publication office.
description: Kalamazoo flora
 extinction_datasetThis file contains
 species names, species characteristics, and species names formatted to
 work with the Phylomatic program for all species included in the Kalamazoo
 flora extinction dataset. The README file includes variable
 descriptions.Kalamazoo flora
 extinction_prairie phylogenetic dataThis file contains the
 branch length for all species from the Kalamazoo flora extinction dataset,
 pulled from Phylomatic.
DOI: 10.5061/dryad.670nh
title: Data from: Young male mating success is associated with sperm number but not with male sex pheromone titres

description: Background: Intraspecific communication is of crucial importance
 throughout the animal kingdom and may involve a combination of visual,
 gustatory, olfactory and acoustic cues. Variation in male sex pheromone
 amount and composition may convey important information to female
 conspecifics, for instance on species identity or age. However, whether
 increased male pheromone titres are associated with fitness benefits for
 the female, thus indicating a role as an honest signal, is under debate.
 Results: Against this background, we tested in the butterfly Bicyclus
 anynana (1) whether young males being successful or unsuccessful in
 gaining a mating differed in sex pheromone titres and (2) for associations
 between male pheromone titres and spermatophore mass, eupyrene sperm
 number, and a variety of female and offspring life-history traits.
 Successful and unsuccessful males did not differ in pheromone titres,
 however eupyrene sperm number was much higher in successful males.
 Pheromone titres were not associated with any fitness-related female or
 offspring trait measured in our study, though correlation analyses yielded
 evidence for trade-offs among specific traits. Patterns did not differ
 among control and olfaction-blocked females. Conclusion: Therefore, we
 suggest that in young B. anynana pheromone titres do not indicate male
 quality.
description: MSP data
 analysisThe package contains the
 raw data/excel files for the two experiments, which were conducted in the
 underlying publication.MSP.rar
DOI: 10.5061/dryad.hf56v
title: Data from: Mining for NRPS and PKS genes revealed a high diversity in the Sphagnum bog metagenome

description: Sphagnum bog ecosystems are among the oldest vegetation forms harboring a
 specific microbial community and are known to produce an exceptionally
 wide variety of bioactive substances. Although the Sphagnum metagenome
 shows a rich secondary metabolism, the genes have not yet been explored.
 To analyze nonribosomal peptide synthetases (NRPSs) and polyketide
 synthases (PKSs), the diversity of NRPS and PKS genes in
 Sphagnum-associated metagenomes was investigated by in silico data mining
 and sequence-based screening (PCR amplification of 9,500 fosmid clones).
 The in silico Illumina-based metagenomic approach resulted in the
 identification of 279 NRPSs and 346 PKSs, as well as 40 PKS-NRPS hybrid
 gene sequences. The occurrence of NRPS sequences was strongly dominated by
 the members of the Protebacteria phylum, especially by species of the
 Burkholderia genus, while PKS sequences were mainly affiliated with
 Actinobacteria. Thirteen novel NRPS-related sequences were identified by
 PCR amplification screening, displaying amino acid identities of 48% to
 91% to annotated sequences of members of the phyla Proteobacteria,
 Actinobacteria, and Cyanobacteria. Some of the identified metagenomic
 clones showed the closest similarity to peptide synthases from
 Burkholderia or Lysobacter, which are emerging bacterial sources of
 as-yet-undescribed bioactive metabolites. This report highlights the role
 of the extreme natural ecosystems as a promising source for detection of
 secondary compounds and enzymes, serving as a source for biotechnological
 applications.
description: NRPS sequences from the
 Sphagnum magellanicum assembled metagenomeNRPS seq Sm metagenome
 assembly.fastaPKS sequences from the
 Sphagnum magellanicum assembled metagenomePKS seq Sm metagenome
 assembly.fastaNRPS-PKS hybrid
 sequences from the Sphagnum magellanicum assembled
 metagenomeNRPS-PKS hybrid seq Sm
 metagenome assembly.fasta
DOI: 10.5061/dryad.b8d60
title: Data from: Intraspecific divergence and evolution of a life-history trade-off along a successional gradient in Hawaii’s Metrosideros polymorpha

description: The importance of environmental gradients in the diversification of
 long-lived tree species is poorly understood. Two morphologically distinct
 varieties of the endemic Hawaiian tree, 'ōhi'a lehua
 (Metrosideros polymorpha), are the canopy dominants at alternate extremes
 of a successional gradient formed by the recurring disturbance of lava
 flows on east Hawai'i Island. The maintenance of these varieties
 despite hybridization may be due to disruptive selection at either end of
 the successional gradient. To test this hypothesis, seeds from three,
 replicate monotypic stands of each variety on east Hawai'i Island
 were germinated and the resulting seedlings grown under four combinations
 of light and nitrogen levels in a greenhouse, and at early- and
 late-successional field sites. Growth and survivorship measures revealed
 differential fitness of these varieties in high- and low-light
 environments in the greenhouse with corresponding differential fitness in
 early- and late-successional field sites. Unique light-by-nitrogen
 interaction effects on growth were observed in each variety, and only the
 late-successional variety appeared to be nitrogen limited. These two
 varieties exhibit the classic plant life-history trade-off between fast
 growth in high light and high survivorship in shade, but notably within a
 single tree species. These findings strongly implicate a role for
 Hawaii's striking environmental heterogeneity in the emergence of at
 least two endemic forms of this woody genus.
description: Raw Data
 MastersheetMastersheet of all raw
 data for greenhouse, field, germination, and fluorometer studies on
 separate excel sheets. A key to all data labels is also added on the fifth
 sheet.Master.xlsx
DOI: 10.5061/dryad.95g1v
title: Data from: Species-area curve and distance-decay relationship indicate habitat thresholds of ectomycorrhizal fungi in an old-growth Pseudotsuga menziesii landscape

description: Aim: Ectomycorrhizal fungi (EMF) are a diverse and essential biota of
 forests that are vulnerable to species loss through reductions in
 late-seral habitat. We examined how the spatial ecology of this biota,
 particularly distance-decay and species-area relationships, could better
 inform habitat thresholds for EMF conservation planning. Location:
 Southeast Vancouver Island near Victoria, British Columbia, Canada.
 Methods: Using a stratified sampling design, 11 plots (0.15 ha in size)
 were established at 0.05 to 17.5 km apart across 2800 ha of mesic
 old-growth Pseudotsuga menziesii var. menziesii and Tsuga heterophylla
 forests. EMF communities were compiled through molecular analysis of root
 tips and sporocarps. Results: The EMF community was comprised of many
 Cortinarius, Piloderma, Russula and Tricholoma species typical of
 mesotrophic habitat. A total of 238 EMF species were observed, of which 86
 species were detected only once. The ratio of average species richness per
 plot (84 taxa) to total richness was low at 0.35, and inherent
 stochasticity of the EMF community was estimated to be 31% community
 dissimilarity for species incidence. Distance decay of EMF communities was
 nonlinear, with an estimated slope break at 2.6 km, followed by a largely
 unchanging trend in β-diversity. Accumulated species-area curves were
 fitted best by the cumulative Weibull sigmoid model, and the asymptote
 (367 species) at approx. 50 ha was consistent with non-parametric
 estimates of γ diversity (342-362 spp.). Main conclusions: Old-growth
 forests host an impressive amount of EMF diversity, and many of the
 Ramaria, Inocybe and Russula species are likely to be endemic to the
 Pacific Northwest. Both niche- and neutral-based processes influenced EMF
 community composition, resulting in a minimum threshold of 50 ha (1.8% of
 the sample area) for capturing γ diversity. These spatial patterns will
 help design and evaluate conservation efforts, such as retention forestry,
 to sustain fully diverse EMF communities over managed landscapes.
description: soil
 chemistryForest floor and upper
 mineral soil (0-20 cm) chemistry analysis for each old-growth
 plotdistance
 matrixInterplot distances
 between old-growth plots used in Mantel testEM fungal
 datasetFull taxa list for each
 old-growth plot, along with Species Hypothesis designation and
 representative molecular sequence
DOI: 10.5061/dryad.n23q7q1
title: Data from: Predator size and prey size-gut capacity ratios determine kill frequency and carcass production in terrestrial carnivorous mammals

description: Carnivore kill frequency is a fundamental part of predator-prey
 interactions, which are important shapers of ecosystems. Current field
 kill frequency data are rare and existing models are insufficiently
 adapted to carnivore functional groups. We developed a kill frequency
 model accounting for carnivore mass, prey mass, pack size, partial
 consumption of prey and carnivore gut capacity. Two main carnivore
 functional groups, small prey-feeders vs large prey-feeders, were
 established based on the relationship between stomach capacity (C) and
 pack corrected prey mass (iMprey). Although the majority of small
 prey-feeders is below, and of large prey-feeders above a body mass of
 10-20 kg, both occur across the whole body size spectrum, indicating that
 the dichotomy is rather linked to body size-related ecology than
 physiology. The model predicts a negative relationship between predator
 size and kill frequency for large prey-feeders. However, for small
 prey-feeders, this negative relationship was absent. When comparing
 carnivore prey requirements to estimated stomach capacity, small
 carnivores may have to eat to their full capacity repeatedly per day,
 requiring fast digestion and gut clearance. Large carnivores do not
 necessarily have to eat to full gastric capacity per day, or do not need
 to eat every day, which in turn reduces kill frequencies or drives other
 ecological processes such as scavenging, kleptoparasitism, and partial
 carcass consumption. Where ecological conditions allow, large prey-feeding
 appears attractive for carnivores, which can thus reduce activities
 related to hunting. This is particularly so for large carnivores, who can
 achieve distinct reductions in hunting activity due to their relatively
 large gut capacity.
description: De Cuyper et
 al_RawDataPredatorPreyRatiosData spreadsheet
 including all raw literature data used for the scaling relationships
 predator size vs prey size, pack size, real observed kill frequency and
 gut capacity (see corresponding tabs). Legends are included to explain
 column headings (see corresponding tabs). Additionally, prey weights
 obtained from internet sources are provided in the
 spreadsheet.
DOI: 10.5061/dryad.h883s
title: Data from: A meta-analysis of the strength and nature of cytoplasmic genetic effects

description: Genetic variation in cytoplasmic genomes (i.e. the mitochondrial genome in
 animals, and the combined mitochondrial and chloroplast genomes in plants)
 was traditionally assumed to accumulate under a neutral equilibrium model.
 This view has, however, come under increasing challenge from studies that
 have experimentally linked cytoplasmic genetic effects to the expression
 of life history phenotypes. Such results suggest that genetic variance
 located within the cytoplasm might be of evolutionary importance and
 potentially involved in shaping population evolutionary trajectories. As a
 step towards assessing this assertion, here we conduct a formal
 meta-analytic review to quantitatively assess the extent to which
 cytoplasmic genetic effects contribute to phenotypic expression across
 animal and plant kingdoms. We report that cytoplasmic effect sizes are
 generally moderate in size and associated with variation across a range of
 factors. Specifically, cytoplasmic effects on morphological traits are
 generally larger than those on life history or metabolic traits.
 Cytoplasmic effect sizes estimated at the between-species scale (via
 interspecies mix-and-matching of cytoplasmic and nuclear genomes) are
 larger than those at the within-species scale. Furthermore, cytoplasmic
 effects tied to epistatic interactions with the nuclear genome tend to be
 stronger than additive cytoplasmic effects, at least when restricting the
 data set to gonochorous animal species. Our results thus confirm that
 cytoplasmic genetic variation is commonly tied to phenotypic expression
 across plants and animals, implicate the cytoplasmic–nuclear interaction
 as a key unit on which natural selection acts and generally suggest that
 the genetic variation that lies within the cytoplasm is likely to be
 entwined in adaptive evolutionary processes.
description: final_raw_dataData file used for meta-analysesmeta-analysis-scriptR-script for full meta-analysismeta_analysis.Rmeta-analysis-script-animals-onlyR-script for gonochorous animal subsetmeta_only_animals.R
DOI: 10.5061/dryad.1ft93
title: Data from: Evolution of increased survival in RNA viruses specialized on cancer-derived cells

description: Viruses and other pathogens can diverge in their evolved host-use
 strategies, due to exposure to different host types and conflicts between
 within-host reproduction and between-host survival. Most host-pathogen
 studies have emphasized the role of intra-host reproduction in the
 evolution of pathogen virulence, whereas the role of extra-host survival
 has received less attention. Here we examined the evolution of free-living
 virion survival in RNA virus populations differing in their histories of
 host-use. To do so, we used lineages of vesicular stomatitis virus (VSV)
 that were experimentally evolved in laboratory tissue culture for 100
 generations on cancer-derived cells, non-cancerous cells, or alternating
 passages of the two host types. We observed that free-living survival
 improved when VSV populations specialized on human cancer-derived (HeLa)
 cells, whereas this trait was not associated with selection on non-cancer
 cells or combinations of the cell types. We attributed this finding to
 shorter-lived HeLa monolayers and/or rapid cell-to-cell spread of viruses
 on HeLa cells in tissue culture, both of which could select for enhanced
 virus stability in between host-cell replenishment. We also showed
 evidence that increases in virion survival were associated with decreases
 in virulence, suggesting a trade-off between survival and virulence for
 the VSV populations on one cell type. Our results shed new light on the
 causes and consequences of "sit and wait" infection strategies
 in RNA viruses.
description: Jan 2013 raw data plaque
 diameterCollected in the
 laboratory (Paul E. Turner lab, Yale University). The plaque diameter data
 for the various virus lineages measured in millimeters. H = HeLa
 specialized. M = MDCK specialized. AH = Alternating generalists propagated
 on HeLa cells. AM = Alternating generalist propagated on MDCK cells.
 Numbers (1, 2, 3, 4) next to virus type corresponds to the lineage (H1,
 M2, etc).Jan 2013 Raw data plaque
 diameter.xlsJan 2013 raw data 37 VSV
 survivalCollected in the
 laboratory (Paul E. Turner lab, Yale University). Microsoft Excel format.
 The virus free-living survival results. H = HeLa specialized. M = MDCK
 specialized. AH = Alternating generalists propagated on HeLa cells. AM =
 Alternating generalist propagated on MDCK cells. Numbers next to virus
 type correspond to lineage of a given virus type (H1, M3,
 etc).Jan
 2013 Raw Data 37 VSV survival
 .xlsJan 2013 raw data cell
 death assayData collected in the
 laboratory (Paul E. Turner lab, Yale University). Microsoft Excel format.
 These are the cell death counts for the two hosts used in the experiment,
 HeLa and MDCK. "Rep" corresponds to
 replicate.Jan 2013 Raw data cell death
 assay.xls
DOI: 10.5061/dryad.3f8v2
title: Data from: Temperature fluctuations during development reduce male fitness and may limit adaptive potential in tropical rainforest Drosophila

description: Understanding the potential for organisms to tolerate thermal stress
 through physiological or evolutionary responses is crucial given rapid
 climate change. Although climate models predict increases in both
 temperature mean and variance, such tolerances are typically assessed
 under constant conditions. We tested the effects of temperature
 variability during development on male fitness in the rainforest fly
 Drosophila birchii, by simulating thermal variation typical of the warm
 and cool margins of its elevational distribution, and estimated
 heritabilities and genetic correlations of fitness traits. Reproductive
 success was reduced for males reared in warm (mean 24°C) fluctuating (±
 3°C) versus constant conditions but not in cool fluctuating conditions
 (mean 17°C), although fluctuations reduced body size at both temperatures.
 Male reproductive success under warm fluctuating conditions was similar to
 that at constant 27°C, indicating that briefly exceeding critical thermal
 limits has similar fitness costs to continuously stressful conditions.
 There was substantial heritable variation in all traits. However,
 reproductive success traits showed no genetic correlation between
 treatments reflecting temperature variation at elevational extremes, which
 may constrain evolutionary responses at these ecological margins. Our data
 suggest that even small increases in temperature variability will threaten
 tropical ectotherms living close to their upper thermal limits, both
 through direct effects on fitness and by limiting their adaptive
 potential.
description: Effect of temperature
 fluctuations on male fitness traits in Drosophila
 birchiiThis Excel file contains
 8 datasheets. Sheets 1-3 are for Experiments I ,II & III, containing
 information about transect, elevation of origin, isofemale line, focal
 male number and treatment. Data are for total cumulative offspring, number
 of matings and offspring per mating. Sheets 4-6 show wing centroid
 measurements for the same experiments respectively. Sheets 7-8 are summary
 line data for Experiments I and II used for heritability estimates and
 genetic correlations.Saxon et al_
 data.xlsx
DOI: 10.5061/dryad.82j66
title: Data from: Food plant-derived disease tolerance and resistance in a natural butterfly-plant-parasite interaction

description: Organisms can protect themselves against parasite-induced fitness costs
 through resistance or tolerance. Resistance includes mechanisms that
 prevent infection or limit parasite growth while tolerance alleviates the
 fitness costs from parasitism without limiting infection. Although
 tolerance and resistance affect host-parasite coevolution in fundamentally
 different ways, tolerance has often been ignored in animal-parasite
 systems. Where it has been studied, tolerance has been assumed to be a
 genetic mechanism, unaffected by the host environment. Here we studied the
 effects of host ecology on tolerance and resistance to infection by
 rearing monarch butterflies on twelve different species of milkweed food
 plants and infecting them with a naturally occurring protozoan parasite.
 Our results show that monarch butterflies experience different levels of
 tolerance to parasitism depending on the species of milkweed that they
 feed on, with some species providing over two-fold greater tolerance than
 other milkweed species. Resistance was also affected by milkweed species,
 but there was no relationship between milkweed-conferred resistance and
 tolerance. Chemical analysis suggests that infected monarchs obtain
 highest fitness when reared on milkweeds with an intermediate
 concentration, diversity and polarity of toxic secondary plant chemicals
 known as cardenolides. Our results demonstrate that environmental factors
 – such as interacting species in ecological food webs – are important
 drivers of disease tolerance.
description: Data from experimentally
 inoculated monarchs on 12 species of milkweed (Asclepias
 sp)Monarch
 data_Host plant 3.txtCardenolide data from 12
 species of milkweed (Asclepias sp)Cardenolide data_Host Plant
 3.txt