cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gg52d
title: Data from: Ecomorphology of the African felid ensemble: the role of the skull and postcranium in determining species segregation and assembling history

description: Morphology of extant felids is regarded as highly conservative. Most
 previous studies have focussed on skull morphology, so a vacuum exists
 about morphofunctional variation in postcranium and its role in
 structuring ensembles of felids in different continents. The African felid
 ensemble is particularly rich in ecologically specialized felids. We
 studied the ecomorphology of this ensemble using 31 cranial and 93
 postcranial morphometric variables measured in 49 specimens of all 10
 African species. We took a multivariate approach controlling for
 phylogeny, with and without body size correction. Postcranial and skull +
 postcranial analyses (but not skull-only analyses) allowed for a complete
 segregation of species in morphospace. Morphofunctional factors
 segregating species included body size, bite force, zeugopodial lengths
 and osteological features related to parasagittal leg movement. A general
 gradient of bodily proportions was recovered: lightly built, long-legged
 felids with small heads and weak bite forces vs. the opposite. Three loose
 groups were recognized: small terrestrial felids, mid-to-large sized
 scansorial felids and specialized Acinonyx jubatus and Leptailurus serval.
 As predicted from a previous study, the assembling of the African felid
 ensemble during the Plio-Pleistocene occurred by the arrival of distinct
 felid lineages that occupied then vacant areas of morphospace, later
 diversifying in the continent.
description: Morales_Giannini_2013_Morphological measurements of African felidsMorphometric measurements of skull and postcranium of African felids. Material was studied in museum collections. For abbreviations of museums and variables see asociated publication (Morales and Giannini, 2013. Ecomorphology of the African felid ensemble: The role of the skull and postcranium in determining species segregation and assembling history). Dataset includs locality and colection dates when available.Morales_Giannini_2013_Database.xlsx
DOI: 10.5061/dryad.fc22r
title: Data from: Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds

description: Birds breeding in heterogeneous landscapes select nest sites by cueing in
 on a variety of factors from landscape features and social information to
 the presence of natural enemies. We focus on determining the relative
 impact of anthropogenic noise on nest site occupancy, compared to amount
 of forest cover, which is known to strongly influence the selection
 process. We examine chronic, industrial noise from natural gas wells
 directly measured at the nest box as well as site-averaged noise, using a
 well-established field experimental system in northwestern New Mexico. We
 hypothesized that high levels of noise, both at the nest site and in the
 environment, would decrease nest box occupancy. We set up nest boxes using
 a geospatially paired control and experimental site design and analyzed
 four years of occupancy data from four secondary cavity-nesting birds
 common to the Colorado Plateau. We found different effects of noise and
 landscape features depending on species, with strong effects of noise
 observed in breeding habitat selection of Myiarchus cinerascens, the
 Ash-throated Flycatcher, and Sialia currucoides, the Mountain Bluebird. In
 contrast, the amount of forest cover less frequently explained habitat
 selection for those species or had a smaller standardized effect than the
 acoustic environment. Although forest cover characterization and
 management is commonly employed by natural resource managers, our results
 show that characterizing and managing the acoustic environment should be
 an important tool in protected area management.
description: Data from: Sound
 settlement: noise surpasses land cover in explaining breeding habitat
 selection of secondary cavity nesting birdsThis file contains all
 data from the paper "Sound settlement: noise surpasses land cover in
 explaining breeding habitat selection of secondary cavity nesting
 birds." Please note, all data from the paper is included in this
 file; however, to analyze site level data for species-inclusive and
 species-specific hypotheses, some simple reorganization will be
 required.kleist_et_al_dryad.csv
DOI: 10.5061/dryad.20h3k
title: Data from: Urgent-start peritoneal dialysis and hemodialysis in ESRD patients: complications and outcomes

description: Background: Several studies have suggested that urgent-start peritoneal
 dialysis (PD) is a feasible alternative to hemodialysis (HD) in patients
 with end-stage renal disease (ESRD), but the impact of the dialysis
 modality on outcome, especially on short-term complications, in
 urgent-start dialysis has not been directly evaluated. The aim of the
 current study was to compare the complications and outcomes of PD and HD
 in urgent-start dialysis ESRD patients. Methods: In this retrospective
 study, ESRD patients who initiated dialysis urgently without a
 pre-established functional vascular access or PD catheter at a single
 center from January 2013 to December 2014 were included. Patients were
 grouped according to their dialysis modality (PD and HD). Each patient was
 followed for at least 30 days after catheter insertion (until January
 2016). Dialysis-related complications and patient survival were compared
 between the two groups. Results: Our study enrolled 178 patients (56.2%
 male), of whom 96 and 82 patients were in the PD and HD groups,
 respectively. Compared with HD patients, PD patients had more
 cardiovascular disease, less heart failure, higher levels of serum
 potassium, hemoglobin, serum albumin, serum pre-albumin, and lower levels
 of brain natriuretic peptide. There were no significant differences in
 gender, age, use of steroids, early referral to a nephrologist, prevalence
 of primary renal diseases, prevalence of co-morbidities, and other
 laboratory characteristics between the groups. The incidence of
 dialysis-related complications during the first 30 days was significantly
 higher in HD than PD patients. HD patients had a significantly higher
 probability of bacteremia compared to PD patients. HD was an independent
 predictor of short-term (30-day) dialysis-related complications. There was
 no significant difference between PD and HD patients with respect to
 patient survival rate. Conclusion: In an experienced center, PD is a safe
 and feasible dialysis alternative to HD for ESRD patients with an urgent
 need for dialysis.
description: relevant
 dataRelevant data underlying
 the results.S1 file_Relevant
 Data.xls
DOI: 10.5061/dryad.4g55s
title: Data from: A pre-breeding immune challenge delays reproduction in the female dark-eyed junco (Junco hyemalis)

description: Precise timing of life-history transitions in predictably changing
 environments is hypothesized to aid in individual survival and
 reproductive success, by appropriately matching an animal's
 physiology and behavior with prevailing environmental conditions.
 Therefore, it is imperative for individuals to time energetically costly
 life-history stages (i.e. reproduction) so they overlap with seasonal
 peaks in food abundance and quality. Female lifetime reproductive fitness
 is affected by several factors that influence energy balance, including
 arrival date, timing of egg production, and energetic condition.
 Therefore, any extra energetic costs during reproduction may negatively
 affect timing of egg production, and ultimately a female's fitness.
 For example, mounting an immunological response elicits a high energetic
 cost, and this transfer of resources towards cell and immune system
 maintenance could have direct negative effects on reproductive timing. In
 order to determine whether an immune challenge delays onset of breeding
 (i.e. egg production), we administered either a humoral immune challenge
 (keyhole limpet hemocyanin (KLH)) (treatment) or physiological saline
 (control) to free-living female dark-eyed juncos (Junco hyemalis) in the
 period immediately prior to egg-laying (~4 weeks). We found that
 KLH-injected females artificially delayed clutch initiation when compared
 to control females. These data help to refine our understanding of how
 free-living birds allocate resources between reproduction and
 self-maintenance processes during the critical pre-laying period of the
 annual cycle.
description: Treated Female
 DataThis data set includes
 date of treatment (KLH or saline), date of the first egg laid (when
 known), female morphometrics, female VLDL levels, and nest
 information.JAB
 Data.xlsNest Success
 DataThis file includes
 nestling mass and tarsus length for each individual nestling across the
 different sampling dates.JAB Nest Success
 Data.xls
DOI: 10.5061/dryad.9pp6q
title: Data from: Genome-wide identification and expression analysis of the ClTCP transcription factors in Citrullus lanatus

description: Background: The plant-specific TCP transcription factor family, which is
 involved in the regulation of cell growth and proliferation, performs
 diverse functions in multiple aspects of plant growth and development.
 However, no comprehensive analysis of the TCP family in watermelon
 (Citrullus lanatus) has been undertaken previously. Results: A total of 27
 watermelon TCP encoding genes distributed on nine chromosomes were
 identified. Phylogenetic analysis clustered the genes into 11 distinct
 subgroups. Furthermore, phylogenetic and structural analyses distinguished
 two homology classes within the ClTCP family, designated Class I and Class
 II. The Class II genes were differentiated into two subclasses, the CIN
 subclass and the CYC/TB1 subclass. The expression patterns of all members
 were determined by semi-quantitative PCR. The functions of two ClTCP
 genes, ClTCP14a and ClTCP15, in regulating plant height were confirmed by
 ectopic expression in Arabidopsis wild-type and ortholog mutants.
 Conclusions: This study represents the first genome-wide analysis of the
 watermelon TCP gene family, which provides valuable information for
 understanding the classification and functions of the TCP genes in
 watermelon.
description: Protein sequences for
 constructing phylogenetic treeAmino acid sequences of
 all the TCP transcription factors in Arabidopsis thaliana(24),
 watermelon(27) and rice(21) were listed to construct phylogenetic
 tree.Data of relative
 chlorophyll content in Arabidopsis leavesData of relative chlorophyll
 content in Arabidopsis
 leaves.xlsInflorescence height
 data of transgenic ArabidopsisPlant height data of
 watermelon treated by GA and CCCPlant height data of watermelon
 treated by GA and CCC.xls
DOI: 10.5061/dryad.8c26c
title: Data from: Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean

description: Knowledge of the scale of dispersal and the mechanisms governing gene flow
 in marine environments remains fragmentary despite being essential for
 understanding evolution of marine biota and to design management plans. We
 use the limpets Patella ulyssiponensis and Patella rustica as models for
 identifying factors affecting gene flow in marine organisms across the
 North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and
 a fragment of the mitochondrial gene cytochrome C oxidase subunit I were
 screened for genetic variation through starch gel electrophoresis and DNA
 sequencing, respectively. An approach combining clustering algorithms with
 clinal analyses was used to test for the existence of barriers to gene
 flow and estimate their geographic location and abruptness. Sharp breaks
 in the genetic composition of individuals were observed in the transitions
 between the Atlantic and the Mediterranean and across southern Italian
 shores. An additional break within the Atlantic cluster separates samples
 from the Alboran Sea and Atlantic African shores from those of the Iberian
 Atlantic shores. The geographic congruence of the genetic breaks detected
 in these two limpet species strongly supports the existence of
 transpecific barriers to gene flow in the Mediterranean Sea and
 Northeastern Atlantic. This leads to testable hypotheses regarding factors
 restricting gene flow across the study area.
description: Patella ulyssiponensis
 allozyme dataPatella_ulyssiponensis_allozyme_data.txtPatella_rustica_allozyme_data
DOI: 10.5061/dryad.4qg5k
title: Data from: Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

description: Successful urban colonisation by formerly rural species represents an
 ideal situation in which to study adaptation to novel environments. We
 address this issue using candidate genes for behavioural traits that are
 expected to play a role in such colonisation events. We identified and
 genotyped 16 polymorphisms in candidate genes for circadian rhythms, harm
 avoidance, and migratory and exploratory behaviour in 12 paired urban and
 rural populations of the blackbird Turdus merula across the Western
 Palearctic. An exonic microsatellite in the SERT gene, a candidate gene
 for harm avoidance behaviour, exhibited a highly significant association
 with habitat type in an analysis conducted across all populations. Genetic
 divergence at this locus was consistent in 10 of the 12 population pairs;
 this contrasts with previously reported stochastic genetic divergence
 between these populations at random markers. Our results indicate that
 behavioural traits related to harm avoidance and associated with the SERT
 polymorphism experience selection pressures during most blackbird
 urbanization events. These events thus appear to be influenced by
 homogeneous adaptive processes in addition to previously reported
 demographic founder events.
description: Genotype and habitat
 type dataMueller_etal_2013_Genotype_Habitattype.txt
DOI: 10.5061/dryad.1h3k8
title: Data from: Long-term agricultural management does not alter the evolution of a soybean-rhizobium mutualism

description: Leguminous crops, like soybeans, often rely on biologically fixed nitrogen
 via their symbiosis with rhizobia rather than synthetic nitrogen inputs.
 However, agricultural management practices may influence the effectiveness
 of biological nitrogen fixation. While the ecological effects of
 agricultural management on rhizobia have received some attention, the
 evolutionary effects have been neglected in comparison. Resource mutualism
 theory predicts that evolutionary effects are likely, however. Both
 fertilization and tillage are predicted to cause the evolution of rhizobia
 that provide fewer growth benefits to plant hosts and fix less nitrogen.
 This study capitalized on an LTER (Long Term Ecological Research)
 experiment that manipulated agricultural management practices in a
 corn-soybean-wheat row crop system for 24 years to investigate whether
 four different management practices (conventional, no-till, low chemical
 input, and certified organic) cause rhizobia populations to evolve to
 become more or less cooperative. We found little evidence that 24 years of
 varying management practices affect the net growth benefits rhizobia
 provide to soybeans, although soybean plants inoculated with soils
 collected from conventional treatments tended to have lower biological
 nitrogen fixation rates than plants inoculated with soils from the
 no-till, low input, and organic management treatments. These findings
 suggest that rhizobia will continue to provide adequate growth benefits to
 leguminous crops in the future, even in intensively managed systems.
description: Experiment 1 Plant
 growth and nodule dataPlant growth and nodule
 data from an experiment in which wildtype and non-nodulating mutant
 soybean plants were inoculated with soils collected from long-term
 agronomic treatments at the Kellogg Biological Station LTER
 site.Schmidt et al 2017 Experiment
 1.csvSchmidt et al 2017
 Experiment 2Plant growth and nodule
 data from an experiment in which wildtype soybean plants were inoculated
 with rhizobium strains isolated from long-term agronomic
 treatments.Schmidt et al 2017
 BNFIsotope data and
 calculations estimating biological nitrogen fixation.Schmidt et al 2007 Data
 analysesSAS code used in the
 analyses presented in Schmidt et al. 2017.
DOI: 10.5061/dryad.17829
title: Data from: Assessment of spatial discordance of primary and effective seed dispersal of European beech (Fagus sylvatica L.) by ecological and genetic methods

description: Spatial discordance between primary and effective dispersal in plant
 populations indicates that postdispersal processes erase the seed rain
 signal in recruitment patterns. Five different models were used to test
 the spatial concordance of the primary and effective dispersal patterns in
 a European beech (Fagus sylvatica) population from central Spain. An
 ecological method was based on classical inverse modelling (SSS), using
 the number of seed/seedlings as input data. Genetic models were based on
 direct kernel fitting of mother-to-offspring distances estimated by a
 parentage analysis or were spatially explicit models based on the genotype
 frequencies of offspring (competing sources model and Moran-Clark's
 Model). A fully integrated mixed model was based on inverse modelling, but
 used the number of genotypes as input data (gene shadow model). The
 potential sources of error and limitations of each seed dispersal
 estimation method are discussed. The mean dispersal distances for seeds
 and saplings estimated with these five methods were higher than those
 obtained by previous estimations for European beech forests. All the
 methods show strong discordance between primary and effective dispersal
 kernel parameters, and for dispersal directionality. While seed rain was
 released mostly under the canopy, saplings were established far from
 mother trees. This discordant pattern may be the result of the action of
 secondary dispersal by animals or density-dependent effects; that is, the
 Janzen-Connell effect.
description: MilleronMEC121049
DOI: 10.5061/dryad.f306q
title: Data from: Evolutionary contribution to coexistence of competitors in microbial food webs

description: The theory of species coexistence is a key concept in ecology that has
 received much attention. The role of rapid evolution for determining
 species coexistence is still poorly understood although evolutionary
 change on ecological time-scales has the potential to change almost any
 ecological process. The influence of evolution on coexistence can be
 especially pronounced in microbial communities where organisms often have
 large population sizes and short generation times. Previous work on
 coexistence has assumed that traits involved in resource use and species
 interactions are constant or change very slowly in terms of ecological
 time-scales. However, recent work suggests that these traits can evolve
 rapidly. Nevertheless, the importance of rapid evolution to coexistence
 has not been tested experimentally. Here, we show how rapid evolution
 alters the frequency of two bacterial competitors over time when grown
 together with specialist consumers (bacteriophages), a generalist consumer
 (protozoan) and all in combination. We find that consumers facilitate
 coexistence in a manner consistent with classic ecological theory.
 However, through disentangling the relative contributions of ecology
 (changes in consumer abundance) and evolution (changes in traits mediating
 species interactions) on the frequency of the two competitors over time,
 we find differences between the consumer types and combinations. Overall,
 our results indicate that the influence of evolution on species
 coexistence strongly depends on the traits and species interactions
 considered.
description: 5SP ciliate
 populations5SP
 Phage
DOI: 10.15468/dl.7xg2eh
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera pardus orientalis"
 ]
}

 The dataset includes 37 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000935-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0145sn6
title: Data from: Seascapes as drivers of herbivore assemblages in coral reef ecosystems

description: Herbivorous fish maintain a critical ecosystem function on coral reefs by
 grazing algae and maintaining highly productive algal turf assemblages.
 Current paradigms implicate habitat complexity, predation and primary
 productivity as major drivers of the distribution and abundance of
 herbivorous fish, yet little is known about the relative contribution of
 these factors. Here, we compare bottom-up and top-down drivers of notional
 herbivore assemblages across an environmental gradient of wave exposure in
 the Palau archipelago. We surveyed herbivore assemblages at reef slopes (6
 - 9m) across 18 sites, and quantified proxies of top-down control
 (predator biomass, habitat complexity) and bottom-up drivers (net primary
 production, nutrients) at each site. Despite substantial variability in
 herbivore biomass throughout the archipelago (6 to 65 g m-2), general
 additive models indicate that neither top-down nor bottom-up drivers
 significantly predicted biomass or density of herbivores among sites. In
 contrast to expectations, herbivore biomass was highest at sites with high
 predator biomass, low structural complexity and low benthic productivity.
 Rather, the highest biomass of herbivores was associated with shallow,
 tidally emergent, productive reef flats located adjacent to steep vertical
 walls (‘drop-offs’). The emergent nature of this neighbouring habitat
 precluded occupation by territorial fishes, and multiple species of
 herbivores were observed to make foraging runs into this habitat once
 tidally inundated. We hypothesize that this habitat configuration provides
 an important cross-habitat resource subsidy. Multivariate ordination and
 permutation of herbivore communities revealed strong evidence for
 biogeographic partitioning throughout the archipelago (western,
 south-western, inner eastern and outer eastern clusters), contributing to
 an emerging picture that the habitat heterogeneity of seascapes can
 overwhelm the effects of conventional top-down and bottom-up structuring
 of herbivory on coral reefs.
description: Roff_Ecological_Monographs_DryadData from: Seascapes as drivers of herbivore assemblages in coral reef ecosystems