cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7264p69
title: Data from: Weighting effective number of species measures by abundance weakens detection of diversity responses

description: 1. The effective number of species (ENS) has been proposed as a robust
 measure of species diversity that overcomes several shortcomings of both
 diversity indices and species richness measures. However, it is not yet
 clear if ENS improves interpretation and comparison of biodiversity
 monitoring data, and ultimately resource management decisions. 2. We used
 simulations of five stream macroinvertebrate assemblages and spatially
 extensive field data of stream fishes and mussels to show (1) how
 different ENS formulations respond to stress and (2) how
 diversity-environment relationships change with values of q, which weight
 ENS measures by species abundances. 3. Values of ENS derived from whole
 simulated assemblages with all species weighted equally (true species
 richness) steadily decreased as stress increased, and ENS-stress
 relationships became weaker and more different among assemblages with
 increased weighting. 4. The amount of variation in ENS across the fish and
 mussel assemblages that was associated with environmental gradients
 decreased with increasing q. 5. Synthesis and applications: ENS does not
 improve interpretability of how diversity responds to stress or natural
 environmental gradients, and incorporating relative abundance into species
 diversity measures as implemented in ENS can actually weaken detection of
 diversity responses. Ecologists need to be cautious about use and
 interpretation of diversity measures whose values are jointly influenced
 by richness and evenness, including ENS, and instead separately assess
 species richness, species evenness, and compositional change in ecological
 communities.
description: Five_assemblagesThis dataset for five macroinvertebrate assemblages is simulated based on large samples collected from minimally-disturbed streams in Pacific Northwest US, and first published in Cao and Hawkins (2005). Each assemblage is consisted of 11 samples (e.g., CM00 - CM10 for Assemblage CM). There are 70 taxa in total across the five assemblages.Tolerance value of 70 taxaThis is a list of tolerance values (TV) for 70 macroinvertebrate taxa in the five assemblages, to general human disturbances in streams of Pacific Northwest US derived based on field data (Cao & Hawkins 2005).TV.txtFish diversity and environmental variablesThis dataset includes the value of effective number of species (ENS) calculated at 21 q-levels (i.e., ENS_0 - ENS_20) and a set of predictor variables describing natural environment, land-uses and spatial connections for 937 stream sites in the State of Illinois, USA.Fish_ENS_Envi.txtMussel diversity and environmental variablesThis dataset includes effective number of species calculated at 21 q-levels (i.e., ENS_0 - ENS_20) for mussel samples collected from 915 stream sites in Illinois, USA, and a set of predictor variables describing natural environment, land-uses and spatial connections.Mussel_ENS_Envi.txt
DOI: 10.5061/dryad.7v87nf5
title: Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits

description: Rising atmospheric CO2 concentrations have increased interest in the
 potential for forest ecosystems and soils to act as carbon (C) sinks.
 While soil organic C contents often vary with tree species identity,
 little is known about if, and how, tree species influence the stability of
 C in soil. Using a 40‐year‐old common garden experiment with replicated
 plots of eleven temperate tree species, we investigated relationships
 between soil organic matter (SOM) stability in mineral soils and 17
 ecological factors (including tree tissue chemistry, magnitude of organic
 matter inputs and their turnover, microbial community descriptors, and
 soil physico‐chemical properties). We measured five SOM stability indices,
 including heterotrophic respiration, C in aggregate‐occluded particulate
 organic matter (POM) and mineral‐associated SOM, and bulk SOM δ15N and
 ∆14C. The stability of SOM varied substantially among tree species and
 this variability was independent of the amount of organic C in soils.
 Thus, when considering forest soils as C sinks, the stability of C stocks
 must be considered in addition to their size. Further, our results suggest
 tree species regulate soil C stability via the composition of their
 tissues, especially roots. Stability of SOM appeared to be greater (as
 indicated by higher δ15N and reduced respiration) beneath species with
 higher concentrations of nitrogen and lower amounts of acid‐insoluble
 compounds in their roots, while SOM stability appeared to be lower (as
 indicated by higher respiration and lower proportions of C in
 aggregate‐occluded POM) beneath species with higher tissue calcium
 contents. The proportion of C in mineral‐associated SOM and bulk soil
 ∆14C, though, were negligibly dependent on tree species traits, likely
 reflecting an insensitivity of some SOM pools to decadal‐scale shifts in
 ecological factors. Strategies aiming to increase soil C stocks may thus
 focus on particulate C pools, which can more easily be manipulated and are
 most sensitive to climate change.
description: Angst_Mueller_GCB_2019_soil_organic_carbon_stability_data This file includes the data for soil clay content, soil chemical properties, and indices of soil organic matter stability as reported in: https://doi.org/10.1111/gcb.14548
DOI: 10.5061/dryad.9p47b7f
title: Data from: Individual variation and seasonality drive bird feeder use during winter in a Mediterranean climate

description: Purposeful provisioning of food to wild animals is a widespread and
 growing activity that has the potential to impact populations and
 communities. Nevertheless, studies assessing use of recreational feeders
 by free-living birds during winter are surprisingly rare and largely
 limited to regions with continental climates characterized by freezing
 temperatures and snow cover. In contrast, there is little information
 available regarding bird use of feeders within warmer climates during
 winter, despite widespread recreational feeding in these areas. In this
 study we quantified visitation patterns to bird feeders in a Mediterranean
 climate to evaluate the relationship between feeder use and several
 environmental variables known to influence supplemental feeder use in
 continental climates. We established a network of bird feeders in
 Corvallis, Oregon, USA that were filled with black oil sunflower
 (Helianthus annuus) seeds and equipped with radio frequency identification
 (RFID) data loggers that recorded &gt;315,000 visits by 70 individual
 Black-capped Chickadees (Poecile atricapillus) across a 5-month period
 (October 2016 – March 2017). We found extensive variation in feeder use,
 with individuals averaging 1 – 406 feeder visits/day and using 1 – 9 of
 the 21 feeders that were available; individual variability was largely
 consistent during the course of our study. At the population level, we
 found that feeder use decreased from the start of our study, and this
 decline continued through the period when foraging was most limited by
 daylight, including the winter solstice. In contrast to theoretical
 predictions and empirical work in continental climates, we found that
 weather variables did not drive feeder use and that feeder visits peaked
 at mid-day and gradually decreased until sunset. Our study indicates that
 individual-level differences combined with seasonality to drive feeder use
 patterns, and we conclude that how birds use supplemental feeders during
 winter in Mediterranean climates appears to differ notably from feeder use
 in continental climates.
description: Daily visits
 dataset1_daily visitsDryad archive dataset
 1_daily.visits.csvDryad archive dataset
 1_metadata_daily.visitsDryad archive dataset
 2_total.feeders.and.visitsDryad archive dataset
 2_metadata_total.feeders.and.visitsDryad archive dataset
 3_vegetationDryad archive dataset
 3_metadata_vegetationDryad archive dataset
 4_visits.since.sunriseDryad archive dataset
 4_metadata_visits.since.sunrise
DOI: 10.5061/dryad.f2979d6
title: Data from: Exposure of avian embryos to cycling incubation temperatures reduces adult bactericidal ability

description: In birds, the temperature at which eggs are incubated shapes many aspects
 of hatchling phenotype, but long-term effects are less studied. We studied
 the effect of incubation temperature and pattern on the subsequent
 development of innate immune function in Japanese quail (Coturnix
 japonica). We incubated quail eggs in one of three replicated treatments:
 Control (37.5°C), Low (36.0°C), and Cyclical incubation. The Cyclical
 treatment had the same average temperature as the Low temperature
 treatment (36.0°C), and an upper temperature that was the same as the
 Control. When individuals were 5-, 20-, and 55-days of age (i.e., adults)
 we measured the ability of blood plasma to kill Escherichia coli.
 Throughout development there was a non- significant trend for immune
 function to be lower in the Cycling treatment. In adulthood however,
 individuals incubated at Cycling temperatures had significantly lower
 immune function than control birds but did not differ from individuals
 incubated at constant low temperatures. Males and females responded
 similarly to the incubation treatment, but females developed a greater
 bactericidal ability than males. We conclude that variation in innate
 immune function of adult birds is shaped by temperature fluctuations
 experienced during incubation.
description: Bacteria killing ability
 dataFILE NAME: Bacteria
 killing ability data File contains bacteria killing ability of plasma
 samples collected from Japanese quail at various days post-hatch (days
 5,20,55). Data were collected by Ben Burrows and Noah Ben-Ezra. Contact
 for data: Gary Burness COLUMN HEADINGS: Trial number: Two trials of the
 experiment were run, 1 (starting September 2014) and 2 (starting December
 2014). Band number: Individual band ID to tell individuals apart.
 Treatment: Incubator temperature treatment (Control = 37.5 Celsius; Low =
 36.0 Celsius; Cyclical = average temperature was 36 Celsius, but the
 temperature was allowed to cycle between 37.5 Celsius and 28 Celsius. Age:
 The age post-hatch at which a blood sample was collected, 1 = day 5
 post-hatch; 2 = day 20 post-hatch; 3 = day 55 post-hatch. Sex: F=female,
 M=male. BKA (%): the percentage of E. coli that were killed (bacteria
 killing ability) when they were added to an individual’s blood plasma. Day
 5 mass (g): Body mass recorded on day 5 (in grams). Day 20 mass (g): Body
 mass recorded on day 20 (in grams). Day 55 mass (g): Body mass recorded on
 day 55 (in grams). Mass (g) stacked: All body mass values (in grams),
 placed in a single column. NOTES: Any additional comments on birds.
 Missing data are reported as blanks.
DOI: 10.5061/dryad.30kk201
title: Data from: Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: comparison between subgroups according to clinical criteria and toxin gene load

description: Data concerning the human microbiota composition during Clostridioides
 (Clostridium) difficile infection (CDI) using next-generation sequencing
 are still limited. We aimed to confirm key features indicating tcdB
 positive patients and compare the microbiota composition between subgroups
 based on toxin gene load (tcdB gene) and presence of significant diarrhea.
 Ninety-nine fecal samples from 79 tcdB positive patients and 20 controls
 were analyzed using 16S rRNA gene sequencing. Chao1 index for alpha
 diversity were calculated and principal coordinate analysis was performed
 for beta diversity using Quantitative Insights into Microbial Ecology
 (QIIME) pipeline. The mean relative abundance in each group was compared
 at phylum, family, and genus levels. There were significant alterations in
 alpha and beta diversity in tcdB positive patients (both colonizer and
 CDI) compared with those in the control. The mean Chao1 index of tcdB
 positive patients was significantly lower than the control group
 (P&lt;0.001), whereas there was no significant difference between tcdB
 groups and between colonizer and CDI. There were significant differences
 in microbiota compositions between tcdB positive patients and the control
 at phylum, family, and genus levels. Several genera such as
 Phascolarctobacterium, Lachnospira, Butyricimonas, Catenibacterium,
 Paraprevotella, Odoribacter, and Anaerostipes were not detected in most
 CDI cases. We identified several changes in the microbiota of CDI that
 could be further evaluated as predictive markers. Microbiota differences
 between clinical subgroups of CDI need to be further studied in larger
 controlled studies.
description: CDI-data
DOI: 10.5061/dryad.sj52ds3
title: Data from: An experimental study of the influence of lithology on compaction behaviour of broken waste rock in coal mine backfill

description: The research aims to explore the influences of lithology on the compaction
 behaviours of broken waste rocks. For this purpose, a WAW1000D servo test
 machine and a self-made bidirectional loading test system for granular
 materials were used to conduct axial and lateral compaction tests on four
 typical types of broken waste rocks: sandstone, mudstone, limestone, and
 shale. On this basis, we analysed the relationships between lateral and
 axial stress with the strain in, and porosity of, the four types of broken
 waste rocks. In addition, the relationship of axial stress with lateral
 stress and lateral pressure coefficient, and the changes in the particle
 size distribution of broken waste rocks before, and after, compaction were
 discussed. The test results demonstrated that the samples of higher
 strength were found to have low lateral and axial strains as well as a
 lower porosity in axial and lateral loading tests; while samples of lower
 strength showed low lateral stress and lateral pressure coefficient under
 axial load. After being compacted, the samples of the four types of broken
 waste rocks were found to have a higher proportion of small particles,
 indicating some particle crushing. Moreover, the samples of lower strength
 were broken to a greater extent.
description: Datadataset-filedata.zip
DOI: 10.5061/dryad.p0544hn
title: Data from: Maternal longevity and offspring sex in wild ungulates

description: In species with sexual size dimorphism, offspring of the larger sex
 usually have greater energy requirements and may lead to greater fitness
 costs for parents. The effects of offspring sex on maternal longevity,
 however, have only been tested in humans. Human studies produced mixed
 results and considerable debate mainly due to the difficulty of
 distinguishing the effects of sexual dimorphism from sociocultural
 factors. To advance this debate, we examined how the relative number of
 sons influenced maternal longevity in four species of free-living
 ungulates (Soay sheep Ovis aries; bighorn sheep, Ovis canadensis; red
 deer, Cervus elaphus; mountain goat, Oreamnos americanus), with high
 male-biased sexual size dimorphism but without complicating sociocultural
 variables. We found no evidence for a higher cumulative cost of sons than
 of daughters on maternal longevity. For a given number of offspring, most
 females with many sons in all four populations lived longer than females
 with few sons. The higher cost of sons over daughters on maternal lifespan
 reported by some human studies may be the exception rather than the rule
 in long-lived iteroparous species.
description: Dataframes used for
 analyses in the paperThe first file includes
 data related to longevity and reproductive success in early life of
 females that survived beyond the onset of actuarial senescence. This data
 was used to produce Table 2 and Figure 1. The second file includes data
 related to longevity and weaning success in early life of females that
 survived beyond the onset of actuarial senescence. This data was used to
 produce Table 3 and Figure 1. The third file includes data related to
 longevity and lifetime reproductive success of adult females. This data
 was used to produce Table 4 and Figure 2. The fourth file includes data
 related to longevity and lifetime weaning success of adult females. This
 data was used to produce Table 5 and Figure 2.data.zip
DOI: 10.5061/dryad.4674nn4
title: Data from: Phylogeography and post-glacial dynamics in the clonal-sexual orchid Cypripedium calceolus L.

description: Aim: We investigated the phylogeographic history of a clonal-sexual
 orchid, to test the hypothesis that current patterns of genetic diversity
 and differentiation retain the traces of climatic fluctuations and of the
 species reproductive system. Location: Europe, Siberia and Russian Far
 East. Taxon: Cypripedium calceolus L. (Orchidaceae). Methods: Samples
 (&gt;900, from 56 locations) were genotyped at eleven nuclear
 microsatellite loci and plastid sequences were obtained for a subset of
 them. Analysis of genetic structure and approximate Bayesian computations
 were performed. Species distribution modelling was used to explore the
 effects of past climatic fluctuations on the species range. Results:
 Analysis of genetic diversity reveals high heterozygosity and allele
 diversity, with no geographical trend. Three genetic clusters are
 identified with extant gene pools derived from ancestral demes in glacial
 refugia. Siberian populations exhibit different plastid haplotypes,
 supporting an early divergence for the Asian gene pool. Demographic
 results based on genetic data are compatible with an admixture event
 explaining differentiation in Estonia and Romania and they are consistent
 with past climatic dynamics inferred through species distribution
 modelling. Current population differentiation does not follow an isolation
 by distance model and is compatible with a model of isolation by
 colonisation. Main conclusions: The genetic differentiation observed today
 in C. calceolus preserves the signature of climatic fluctuations in the
 historical distribution range of the species. Our findings support the
 central role of clonal reproduction in in reducing loss of diversity
 through genetic drift. The dynamics of the clonal-sexual reproduction are
 responsible for the persistence of ancestral variation and stability
 during glacial periods and post-glacial expansion.
description: Microsatellite
 datasetGenotypes at eleven loci
 for 904 individuals.In
 DRYAD.xlsx
DOI: 10.5061/dryad.v4p9g28
title: Data from: Population genomic evidence reveals subtle patterns of differentiation in the trophically polymorphic Cuatro Ciénegas cichlid, Herichthys minckleyi

description: In recent decades, an increased understanding of molecular ecology has led
 to a reinterpretation of the role of gene flow during the evolution of
 reproductive isolation and biological novelty. For example, even in the
 face of ongoing gene flow strong selection may maintain divergent
 polymorphisms, or gene flow may introduce novel biological diversity via
 hybridization and introgression from a divergent species. Herein, we
 elucidate the evolutionary history and genomic basis of a trophically
 polymorphic trait in a species of cichlid fish, Herichthys minckleyi. We
 explored genetic variation at three hierarchical levels; between H.
 minckleyi (n=69) and a closely related species H. cyanoguttatus (n=10),
 between
description: Hminck_StandardizedTSStandardized tooth size and individual ID's for Herichthys minckleyi.Bell_etal_2018_STS.csv
DOI: 10.5061/dryad.dv4vk6c
title: Data from: The effects of different cold-temperature regimes on development, growth, and susceptibility to an abiotic and biotic stressor

description: 1. Global climate change is expected to both increase average temperatures
 as well as temperature variability. 2. Increased average temperatures has
 led to earlier breeding in many spring-breeding organisms. However,
 individuals breeding earlier will also face increased temperature
 fluctuations, including exposure to potentially harmful cold temperature
 regimes during early developmental stages. 3. Using a model
 spring-breeding amphibian, we investigated how embryonic exposure to
 different cold-temperature regimes (control, cold-pulse, and cold-press)
 affected (1) compensatory larval development and growth, (2) larval
 susceptibility to a common contaminant, and (3) larval susceptibility to
 parasites. 4. We found: (1) no evidence of compensatory development or
 growth, (2) larvae exposed to the cold-press treatment were more
 susceptible to NaCl at 4-d post-hatching but recovered by 17-d
 post-hatching, and (3) larvae exposed to both cold treatments were less
 susceptible to parasites. 5. These results demonstrate that variation in
 cold-temperature regimes can lead to unique direct and indirect effects on
 larval growth, development, and response to stressors. This underscores
 the importance of considering cold temperature variability and not just
 increased average temperatures when examining the impacts of climate
 disruption.
description: Wersebe et al.
 2019_Ecology and Evolution_DryadFile includes data on
 (1) mass/development of tadpoles across three time points, (2)
 susceptibility of tadpoles to NaCl (time to death assay), and (3)
 susceptibility of tadpoles to trematodes (parasite
 assay).
DOI: 10.5061/dryad.2g6p534
title: Data from: Breeding success but not mate choice is phenotype- and context-dependent in a color polymorphic raptor

description: Morph-specific mate choice has been proposed as one of the evolutionary
 mechanisms that contribute to the maintenance of variation in color
 polymorphic systems. Coloration usually covaries with other phenotypic
 traits affecting life history and thus is often used as a criterion for
 mate choice. Here, we assess whether mating patterns, natal dispersal, and
 breeding output are phenotype-dependent in the color polymorphic
 Eleonora’s falcon. We used a long-term dataset of 946 individually ringed
 adult falcons that included 109 individuals monitored from birth up to
 recruitment into the breeding population. Overall, patterns of mate choice
 with regard to coloration were neither assortative nor disassortative.
 Natal dispersal distance was greater in females but was not associated
 with coloration. Breeding success was both morph-dependent and
 context-dependent. Although clutch size was similar in differently colored
 pairs, differences arose in the number of chicks that fledge. In some
 years, dark males raised more offspring, regardless of female color morph.
 Differences in the breeding tactics between male morphs could be
 associated with intraspecific predation and may thus contribute to the
 observed differences in breeding output, especially when food availability
 is low. This suggests that mating patterns may interact with other factors
 and give rise to the observed higher breeding output of dark males only
 under certain environmental conditions.
description: DatasetDataset used in the analysis of breeding output of the color polymorphic Eleonora's falcon