cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v6g985s
title: Data from: Anthropogenic mining alters macroinvertebrate size spectra in streams

description: 1. Food web properties can to be used in bioassessment as indicators of
 ecosystem stress, although logistical constraints restrict their
 widespread use. Size spectra (body mass – abundance relationships) are
 easier to produce, still incorporate much of the variation in feeding
 interactions and indicate the strength of the energy transfer efficiency.
 2. Here we examined the effect of acid mine drainage on the size spectra
 of stream macroinvertebrate communities in 25 New-Zealand streams with a
 comparative survey. We predicted that the largest sized organisms would be
 most susceptible to acid mine drainage, leading to a reduction in their
 abundances and associated decrease in the range of body sizes present
 across the gradient, as well as a reduction in total community abundance.
 3. The largest sized organisms were more sensitive to inputs of acid mine
 drainage, and were absent at the most affected sites. Surprisingly, the
 smallest body sizes were also removed by acid mine drainage. This led to a
 reduction of up to two orders of magnitude in the range of body sizes
 present in mine impacted sites. Total community abundance decreased along
 the impact gradient. 4. The changes in size spectra were also associated
 with changes in the proportion of functional feeding groups, suggesting
 concomitant changes in food web structure. Specifically communities became
 dominated by collector browsers and small bodied predators across the
 gradient. The simplification of the food web structure suggests that
 communities may be dominated by a few strong energy pathways, lowering
 their functionality and stability. However, the loss of large bodied
 predators also reduces top down pressure, likely increasing community
 stability. Further research is needed to elucidate the cumulative effects
 of these interacting processes.
description: estimated_dwThis file contains the estimated dry weight for all individual macroinvertebrates collected across 25 streams in New Zealand. Below are the column names and a brief description of them. site = Site name; character string. surber = Surber sample that individual was collected in (s1, s2, or s3). linear_meas = linear measurement of the individual in millimeters. dw = estimated dry weight of individual in units of grams. FFG = functional feeding group; CB = collector browser, G = grazer, P = predator, FF = filter feeder, S = shredder, O = omnivore, NA = unknown.gradient_chemistryThis file contains chemical data for 25 streams in New Zealand across an acid mine drainage gradient. pH and conductivity were recorded in the field using standard meters (YSI 550A & YSI 63). Element concentrations were estimated using ICPMS analysis of a filtered (pore size = 0.45 um) water sample collected in the field. site = site name. cond = specific conductivity (microsiemens per centimeter). Elemental concentrations are reported in micrograms per liter.
DOI: 10.5061/dryad.st350
title: Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

description: Animal movement is fundamental for ecosystem functioning and species
 survival, yet the effects of the anthropogenic footprint on animal
 movements have not been estimated across species. Using a unique
 GPS-tracking database of 803 individuals across 57 species, we found that
 movements of mammals in areas with a comparatively high human footprint
 were on average one-half to one-third the extent of their movements in
 areas with a low human footprint. We attribute this reduction to
 behavioral changes of individual animals and to the exclusion of species
 with long-range movements from areas with higher human impact. Global loss
 of vagility alters a key ecological trait of animals that affects not only
 population persistence but also ecosystem processes such as predator-prey
 interactions, nutrient cycling, and disease transmission.
description: Terrestrial Mammal
 Displacement DataThis data file includes
 median (0.5 quantile) and long-distance (0.95 quantile) displacement
 distances for 803 individuals spanning 57 terrestrial mammal species. Also
 included are mean body mass, trophic guild, mean Normalised Difference
 Vegetation Index (NDVI) and mean human footprint index values for each
 individual. Displacement values are in kilometres and body mass values are
 in grams. The displacement and body mass values are log10 transformed and
 the NDVI values are scaled. Please note that each row within a time
 interval represents a different individual. Please see the associated
 manuscript and supplementary materials for details on the data sources and
 calculation methods.MammalDisplacementData.csv
DOI: 10.5061/dryad.85n4k
title: Data from: Heterozygosity-fitness correlation at the major histocompatibility complex despite low variation in Alpine ibex (Capra ibex)

description: Crucial for the long-term survival of wild populations is their ability to
 fight diseases. Disease outbreaks can lead to severe population size
 reductions, which makes endangered and reintroduced species especially
 vulnerable. In vertebrates, the major histocompatibility complex (MHC)
 plays an important role in determining the immune response. Species which
 went through severe bottlenecks, often show very low levels of genetic
 diversity at the MHC. Due to the known link between the MHC and immune
 response, such species are expected to be at particular risk in case of
 disease outbreaks. However, so far, only few studies have shown that low
 MHC diversity is correlated with increased disease susceptibility in
 species after severe bottlenecks. We investigated genetic variation at the
 MHC and its correlations with disease resistance and other fitness related
 traits in Alpine ibex (Capra ibex), a wild goat species that underwent a
 strong bottleneck in the last century and that is known to have extremely
 low genetic variability, both genome-wide and at the MHC. We studied MHC
 variation in male ibex of Gran Paradiso National Park, the population used
 as source for all post-bottleneck reintroductions. We found that
 individual MHC heterozygosity (based on six microsatellites) was not
 correlated with genome-wide neutral heterozygosity. MHC heterozygosity,
 but not genome-wide heterozygosity, was positively correlated with
 resistance to infectious kerato-conjunctivitis and with body mass. Our
 results show that genetic variation at the MHC plays an important role in
 disease resistance and, hence, should be taken into account for
 successfully managing species conservation.
description: heterozygosity-fitnessthe file contains Standardized multilocus heterozygosity calculated at 37 putatively neutral markers as well as at 6 MHC-linked markers and fitness data of 147 male Alpine ibex of Gran Paradiso National Park (Italy). Please note that fitness data were only available for a subset of the genotyped individuals. The heterozygosity-fitness correlations were therefore based only on 147 out of the 247 individuals in file "genotypes_PNGP". The full dataset was however used for the calculations of diversity measures and also for the Standardized multilocus heterozygosity that was calculated for each individual as the ratio of its heterozygosity to the mean heterozygosity in the population of the loci at which the individual was genotyped (Coltman et al., 1999).genotypes_PNGPThe file contains microsatellite genotype data. 6 MHC-linked and 37 putatively neutral markers.heterozygosity-IKCThe file contains individual kerato conjunctivitis dataset.
DOI: 10.5061/dryad.qm288
title: Data from: The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages

description: Conservation of ecological communities requires deepening our
 understanding of genetic diversity patterns and drivers at community-wide
 scales. Here we use seascape genetic analysis of a diversity metric,
 allelic richness, for 47 reef species sampled across 13 Hawaiian Islands
 to empirically demonstrate that large reefs high in coral cover harbor the
 greatest genetic diversity on average. We found that a species’ life
 history (e.g., depth range and herbivory) mediates response of genetic
 diversity to seascape drivers in logical ways. Further, a metric of
 combined multi-species allelic richness showed strong coupling to species
 richness and habitat area, quality and stability that few species showed
 individually. We hypothesize that macroecological forces and species
 interactions, by mediating species turnover and occupancy and thus a
 site’s mean effective population size, influence the aggregate genetic
 diversity a site, potentially allowing it to behave as an apparent
 emergent trait that is shaped by the dominant seascape drivers. The
 results highlight inherent feedbacks between ecology and genetics, raise
 concern that genetic resilience of entire reef communities is compromised
 by factors that reduce coral cover or available habitat, including thermal
 stress, and provide a foundation for new strategies for monitoring and
 preserving biodiversity of entire reef ecosystems.
description: ToBoLab Hawaii reef
 genetic data files Arlequin formatEach file is named with
 the first three letters of the genus and species names followed by a two
 letter marker abbreviation, the number of loci when more than one, and the
 last name of the original data owner. In each file, island sampling
 locations are indicated by the first four letters of the island name. For
 files using a HaplotypeDefinition List, formatting changes to this section
 may be needed to successfully load into Arlequin. Use PGDSpider software
 to reformat files to a different input format. Please contact data owners
 before use of these datasets to obtain detailed information about sampling
 and study design for proper interpretation of findings. See Appendix in
 the Supplementary materials of the study for full names and addresses of
 data ownersGenetic Datasets
 DRYAD.zipSelkoe Supplementary
 data R-2Datasets S1-S7
 accompanying Selkoe et al. 2016 ProcB
 http://dx.doi.org/10.1098/rspb.2016.0354
DOI: 10.5061/dryad.b56n0
title: Data from: Persistent inter- and intraspecific gene exchange within a parallel radiation of caterpillar hunter beetles (Calosoma sp.) from the Galápagos

description: When environmental gradients are repeated on different islands within an
 archipelago, similar selection pressures may act within each island,
 resulting in the repeated occurrence of ecologically similar species on
 each island. The evolution of ecotypes within such radiations may either
 result from dispersal, that is each ecotype evolved once and dispersed to
 different islands where it colonized its habitat, or through repeated and
 parallel speciation within each island. However, it remains poorly
 understood how gene flow during the divergence process may shape such
 patterns. In the Galápagos islands, three phenotypically similar species
 of the beetle genus Calosoma occur at higher elevations of different
 islands, while lowlands are occupied by a fourth species. By genotyping
 all major populations within this radiation for two nuclear and three
 mitochondrial gene fragments and seven microsatellite markers, we found
 strong support that the oldest divergence separates the highland species
 of the oldest island from the remaining species. Despite their
 morphological distinctness, highland species of the remaining islands were
 genetically closely related to the lowland population on each island and
 within the same magnitude as lowland populations sampled at different
 islands. Repeated evolution of highland ecotypes out of the lowland
 species appears the most likely scenario and estimates of geneflow rates
 revealed extensive admixture among ecotypes within islands, as well as
 between islands. These findings indicate that gene exchange among the
 different populations and species may have shaped the phylogenetic
 relationships and the repeated evolution of these ecotypes.
description: Calo_µsatsRaw micosatellite genotypesCalo_IMa2Input file of IMa2 analysisCalo_CAD_haplos.treesBEAST v1.8.0 and TreeAnnotator v1.80.0 output files for the nuclear genes cad.Calo_Enolase_haplos.treesBEAST v1.8.0 and TreeAnnotator v1.80.0 output files for the nuclear gene cad.Calo_mtDNA_haplos.treesBEAST v1.8.0 and TreeAnnotator v1.80.0 output files for the concatenated mtDNA.Calo_CAD_haplos.infoList of individuals in which each cad haplotype was found.Calo_Enolase_haplos.infoList of individuals in which each enolase haplotype was found.
DOI: 10.15468/dl.md4bu3
title: Occurrence Download

description: A dataset containing 30661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.12_1",
 "OccurrenceStatus is Present",
 "Year 1893-1933"
 ]
}

 The dataset includes 30661 records from 236 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000546-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15482/usda.adc/29621015
title: Data from: Extrusion processing improves rainbow trout digestibility of microalgal <i>Nannochloropsis oculata</i> co-product biomass for more sustainable aquaculture diets

description: Aquaculture feeds include fishmeal (FM) and fish oil (FO), derived from wild-caught marine fish such as anchovy and sardines, and pose ecological, food security, and economic drawbacks for sustainable aquaculture, the world's fastest-growing agricultural sector. Protein-rich microalgal co-product is a promising alternative to unsustainably sourced fishmeal in aquaculture diets. Microalgal co-product is a defatted biomass left over after extracting omega-3-rich oil for human nutraceuticals and crude oil for fuels. In this study, we report the first evaluations of nutritive values and digestibility of raw, extrusion- and enzymatic-processed co-product of the marine microalga <i>Nannochloropsis</i><i> </i><i>oculata</i> (<i>N. oculata</i> co-product). Results allowed us to evaluate the feasibility of using processed biomass in aquafeed for rainbow trout (<i>Oncorhynchus mykiss</i>), an important model for all salmonid aquaculture. Extrusion processing temperature (90 °C vs 127 °C) influenced the nutritional value of <i>N. oculata</i>. Protein and energy levels were significantly higher in co-product from both extrusion temperature treatments than in non-extruded raw co-product. Essential amino acid levels did not differ between extrusion temperatures, except that methionine was significantly lower in coproduct from 127 °C extrusion processing than from 90 °C extrusion processing. The protein level in extrusion processed co-product was not significantly influenced by pre-cooking. We detected the highest digestibility of crude protein, energy, most of the amino acids, and omega 3 polyunsaturated fatty acids (n3 PUFA) in extruded (90 °C) <i>N. oculata</i> co-product ingredient. Nutrient digestibility of enzymatic processed <i>N. oculata</i> co-product were mostly the same as extrusion processing or lower for certain nutrients. Overall, extrusion processing of <i>N. oculata</i> at 90 °C provided the best outcome for digestible protein, and yielded an excellent source of digestible protein, amino acids, and long chain omega-3 profile for rainbow trout and which could be an alternative to replace fishmeal in rainbow trout diets.
DOI: 10.15482/usda.adc/29621015.v1
title: Data from: Extrusion processing improves rainbow trout digestibility of microalgal <i>Nannochloropsis oculata</i> co-product biomass for more sustainable aquaculture diets

description: Aquaculture feeds include fishmeal (FM) and fish oil (FO), derived from wild-caught marine fish such as anchovy and sardines, and pose ecological, food security, and economic drawbacks for sustainable aquaculture, the world's fastest-growing agricultural sector. Protein-rich microalgal co-product is a promising alternative to unsustainably sourced fishmeal in aquaculture diets. Microalgal co-product is a defatted biomass left over after extracting omega-3-rich oil for human nutraceuticals and crude oil for fuels. In this study, we report the first evaluations of nutritive values and digestibility of raw, extrusion- and enzymatic-processed co-product of the marine microalga <i>Nannochloropsis</i><i> </i><i>oculata</i> (<i>N. oculata</i> co-product). Results allowed us to evaluate the feasibility of using processed biomass in aquafeed for rainbow trout (<i>Oncorhynchus mykiss</i>), an important model for all salmonid aquaculture. Extrusion processing temperature (90 °C vs 127 °C) influenced the nutritional value of <i>N. oculata</i>. Protein and energy levels were significantly higher in co-product from both extrusion temperature treatments than in non-extruded raw co-product. Essential amino acid levels did not differ between extrusion temperatures, except that methionine was significantly lower in coproduct from 127 °C extrusion processing than from 90 °C extrusion processing. The protein level in extrusion processed co-product was not significantly influenced by pre-cooking. We detected the highest digestibility of crude protein, energy, most of the amino acids, and omega 3 polyunsaturated fatty acids (n3 PUFA) in extruded (90 °C) <i>N. oculata</i> co-product ingredient. Nutrient digestibility of enzymatic processed <i>N. oculata</i> co-product were mostly the same as extrusion processing or lower for certain nutrients. Overall, extrusion processing of <i>N. oculata</i> at 90 °C provided the best outcome for digestible protein, and yielded an excellent source of digestible protein, amino acids, and long chain omega-3 profile for rainbow trout and which could be an alternative to replace fishmeal in rainbow trout diets.
DOI: 10.5061/dryad.643r37b
title: Data from: Variation in individual temperature preferences, not behavioural fever, affects susceptibility to chytridiomycosis in amphibians

description: The ability of wildlife populations to mount rapid responses to novel
 pathogens will be critical for mitigating the impacts of disease outbreaks
 in a changing climate. Field studies have documented that amphibians
 preferring warmer temperatures are less likely to be infected with the
 fungal pathogen Batrachochytrium dendrobatidis (Bd). However, it is
 unclear whether this phenomenon is driven by behavioural fever or natural
 variation in thermal preference. Here, we placed frogs in thermal
 gradients, tested for temperature preferences and measured Bd growth,
 prevalence, and the survival of infected animals. Although there was
 significant individual- and species-level variation in temperature
 preferences, we found no consistent evidence of behavioural fever across
 five frog species. Interestingly, for species that preferred warmer
 temperatures, the preferred temperatures of individuals were negatively
 correlated with Bd growth on hosts, while the opposite correlation was
 true for species preferring cooler temperatures. Our results suggest that
 variation in thermal preference, but not behavioural fever, might shape
 the outcomes of Bd infections for individuals and populations, potentially
 resulting in selection for individual hosts and host species whose
 temperature preferences minimize Bd growth and enhance host survival
 during epidemics.
description: Bd thermoregulation data
 and code Sauer_ErinMetadata can be found in
 the first worksheet of the workbook.
DOI: 10.5061/dryad.43b8h
title: Data from: The biogeography of Knightiella splachnirima

description: A comprehensive, geo-referenced compilation of the known global
 distribution of Knightiella splachnirima is presented, based on public
 herbarium records, literature records, and personal observations from New
 Zealand, Tasmania and Victoria. It appears likely that K. splachnirima has
 a much wider distribution within New Zealand than current records show.
description: Tables - Ludwig (2016)
 K. splachnirima BiogeographySeven tables comprising
 collection details, including geographic coordinates, of all available
 records (herbarium specimens and literature records) of Knightiella
 splachnirima.
DOI: 10.5061/dryad.bn3kd
title: Data from: Demography of Euterpe precatoria and Mauritia flexuosa in the Amazon: application of integral projection models for their harvest

description: Non-Timber Forest Products like palm fruits are fundamental in the
 livelihood of Amerindian groups. For the last 10 years the fruits of wild
 palm species, like Euterpe precatoria and Mauritia flexuosa, have been
 entering into global markets. These species are mostly harvested felling
 the adults, a practice that may have a disproportionate impact in the
 conservation of the populations. We studied the demography of E.
 precatoria and M. flexuosa, two important palms of the Amazon, using
 integral projection models, to characterize the population dynamics and
 project impact of different fruit harvest methods: adult felling and
 direct fruit harvest. We followed over 1400 individuals from populations
 with low harvest intensities in the Tikuna community of Amacayacu,
 Amazonas, Colombia from 2011 to 2013, establishing four plots for E.
 precatoria in seasonally inundated forests and two for M. flexuosa in
 swamps. The population growth in E. precatoria was slightly declining,
 whereas M. flexuosa was stable. As expected, the simulations of adult
 felling diminished λ and the number of available adults under any scenario
 for either species. On the contrary, the simulations support existing
 information that climbing and other non-destructive harvest methods would
 probably allow a sustainable management, satisfying the demand and
 preserving wild populations.
description: Demographic data of two
 palm species of the AmazonThe sheet datep contains
 data of Euterpe precatoria, the sheet datmf contains data of Mauritia
 flexuosa. Both sheets have data of: plot, individuals, size category,
 survival, stem appearance, height and height increase, number of leaves
 produced, number of pinnae in time t, number of pinnae in time t+1,
 fertility and number of racemes produced. The sheet sedep contains data of
 Euterpe precatoria germinated seedlings in the last census and so does the
 sheet seedmf, but for Mauritia flexuosa. The two sheets contain
 information of plot, survival, number of leaves produced, number of pinnae
 in time t and number of pinnae in time t+1datamazonpalms.xls