cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.577t4d00
title: Data from: The effect of a competitor on a model adaptive radiation

description: The ecological forces shaping adaptive radiations are of great interest to
 evolutionary ecologists. Here we experimentally test the hypothesis that
 the diversification of a lineage should be limited in the presence of
 competition from another taxon. We do this by studying a model microbial
 adaptive radiation (the generation of phenotypic diversity in asexual
 lineages of the bacterium Pseudomonas fluorescens) in the presence or
 absence of a competitor (Pseudomonas putida). In a spatially heterogeneous
 environment, the competitor P. putida reduced P. fluorescens population
 size only slightly, and had no effect on diversification. In a spatially
 homogeneous environment the competitor reduced P. fuoresecens population
 size to a much greater extent. Again the final extent of diversification
 in P. fluorescens was not affected by the competitor, but early
 diversification was accelerated. In this environment P. putida suppressed
 the growth of a common variant of P. fluorescens and directly or
 indirectly facilitated the growth of a rare morph. Our results suggest
 that competition experienced by diversifying lineages may have complex
 effects on adaptive radiations not fully captured by current theory.
description: Zhang_et_al_Evol_dataExcel file including all raw data for the publication, with detailed description within each spreadsheet.
DOI: 10.5061/dryad.q3d0n
title: Data from: On the importance of shrub encroachment by sprouters, climate, species richness and anthropic factors for ecosystem multifunctionality in semi-arid mediterranean ecosystems

description: One of the most important changes taking place in drylands worldwide is
 the increase of the cover and dominance of shrubs in areas formerly devoid
 of them (shrub encroachment). A large body of research has evaluated the
 causes and consequences of shrub encroachment for both ecosystem structure
 and functioning. However, there are virtually no studies evaluating how
 shrub encroachment affects the ability of ecosystems to maintain multiple
 functions and services simultaneously (multifunctionality). We aimed to do
 so by gathering data from ten ecosystem functions linked to the
 maintenance of primary production and nutrient cycling and storage
 (organic C, activity of β-glucosidase, pentoses, hexoses, total N, total
 available N, amino acids, proteins, available inorganic P, and phosphatase
 activity), and summarizing them in a multifunctionality index (M). We
 assessed how climate, species richness, anthropic factors (distance to the
 nearest town, sandy and asphalted road, and human population in the
 nearest town at several historical periods) and encroachment by sprouting
 shrubs impacted both the functions in isolation and M along a regional
 (ca. 350 km) gradient in Mediterranean grasslands and shrublands dominated
 by a non-sprouting shrub. Values of M were higher in those grasslands and
 shrublands containing sprouting shrubs (43 and 62%, respectively). A
 similar response was found when analyzing the different functions in
 isolation, as encroachment by sprouting shrubs increased functions by
 2–80% compared to unencroached areas. Encroachment was the main driver of
 changes in M along the regional gradient evaluated, followed by anthropic
 factors and species richness. Climate had little effects on M in
 comparison to the other factors studied. Similar responses were observed
 when evaluating the functions in isolation. Overall, our results showed
 that M was higher at sites with higher sprouting shrub cover, longer
 distance to roads and higher perennial plant species richness. Our study
 is the first documenting that ecosystem multifunctionality in shrublands
 is enhanced by encroaching shrubs differing in size and leaf attributes.
 Our findings reinforce the idea that encroachment effects on ecosystem
 functioning cannot be generalized, and that are largely dependent on the
 traits of the encroaching shrub relative to those of the species being
 replaced.
description: Quero et al 2013
 Ecosystems
DOI: 10.5061/dryad.3m1v4
title: Data from: Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities

description: 1. It is well-known that vascular plants have species-specific effects on
 soil properties. However, little is known on how individual species
 forming biocrusts, communities dominated by lichens, mosses and
 cyanobacteria that are prevalent in many ecosystems world-wide, affect
 microbial communities and soil variables related to nutrient cycling. 2.
 We evaluated the relationship of six biocrust-forming lichens (Buellia
 epipolia, Diploschistes diacapsis, Fulgensia subbracteata, Psora
 decipiens, Squamarina cartilaginea and Squamarina lentigera) with
 microbial abundance and multiple variables associated with soil nitrogen
 (N), carbon (C) and phosphorus (P) cycling and storage. We also evaluated
 whether the composition of lichen tissues (contents in C, N, P and
 polyphenols) is related to the C, N, P availability and microbial
 abundance in soils. Finally, we assessed what lichen species positively
 and negatively relate to soil fertility compared to bare ground areas
 without biocrusts. 3. We found contrasted C, N, P availability and soil
 microbial abundance under the different biocrust-forming lichens.
 Interestingly, inorganic P and amino acids were the most important factors
 differentiating lichen microsites. These differences in nutrient
 availability seem to be related to the C, N and P composition of the
 lichen tissues. For example, soils under D. diacapsis and P. decipiens,
 which had the lowest and highest C, N and P contents in their tissues,
 respectively, had the lowest and highest nutrient availability,
 respectively. We also found contrasted soil microbes abundance under the
 different soil lichens. For instance, F. subbracteata and D. diacapsis
 were negatively related to the abundance of bacteria compared to bare
 ground areas. 4. Our results support the idea that, as found with vascular
 plants, biocrust-forming lichens have species-specific effects on soil
 microbial communities and C, N and P cycling. Thus, continuing considering
 biocrusts as a unique entity will only add confusion to our knowledge of
 how they control nutrient availability and microbial abundance in the
 ecosystems where this key community is prevalent.
description: Dataset
DOI: 10.5061/dryad.4md11
title: Data from: Oxidant trade-offs in immunity: an experimental test in a lizard

description: Immune system functioning and maintenance entails costs which may limit
 investment into other processes such as reproduction. Yet, the proximate
 mechanisms and ‘currencies’ mediating the costs of immune responses remain
 elusive. In vertebrates, up-regulation of the innate immune system is
 associated with rapid phagocytic production of pro-oxidant molecules
 (so-called ‘oxidative burst’ responses). Oxidative burst responses are
 intended to eliminate pathogens but may also constitute an
 immunopathological risk as they may induce oxidative damage to self cells.
 To minimize the risk of infection and, at the same time, damage to self,
 oxidative burst activity must be carefully balanced. The current levels of
 pro- and antioxidants (i.e. the individual oxidative state) is likely to
 be a critical factor affecting this balance, but this has not yet been
 evaluated. Here, we perform an experiment on wild-caught painted dragon
 lizards (Ctenophorus pictus) to examine how the strength of
 immune-stimulated oxidative burst responses of phagocytes in whole blood
 relates to individual oxidative status under control conditions and during
 an in vivo immune challenge with Escherichia coli lipopolysaccharide
 (LPS). Under control conditions, oxidative burst responses were not
 predicted by the oxidative status of the lizards. LPS-injected individuals
 showed a strong increase in pro-oxidant levels and a strong decrease in
 antioxidant levels compared to control individuals demonstrating a shift
 in the pro-/antioxidant balance. Oxidative burst responses in LPS-injected
 lizards were positively related to post-challenge extracellular
 pro-oxidants (reflecting the level of cell activation) and negatively
 related to pre-challenge levels of mitochondrial superoxide (suggesting an
 immunoregulatory effect of this pro-oxidant). LPS-challenged males had
 higher oxidative burst responses than females, and in females oxidative
 burst responses seemed to depend more strongly on antioxidant status than
 in males. Our results confirm the idea that oxidative state may constrain
 the activity of the innate immune system. These constraints may have
 important consequences for the way selection acts on pro-oxidant
 generating processes.
description: Oxidant trade-offs in
 painted dragonsburstpictus Plos
 one.xls
DOI: 10.5061/dryad.v051c
title: Data from: Here's to the losers: evolvable residents accelerate the evolution of high fitness invaders

description: Recent work has shown that evolvability plays a key role in determining
 the long-term population dynamics of asexual clones. However, simple
 considerations suggest that the evolvability of a focal lineage of
 bacteria should also be influenced by the evolvability of its competitors.
 First, evolvable competitors should accelerate evolution by impeding the
 fixation of the focal lineage through a clonal interference–like
 mechanism. Second, evolvable competitors should increase the strength of
 selection by rapidly degrading the environment, increasing selection for
 adaptive mutations. Here we tested these ideas by allowing a high-fitness
 clone of the bacterium Pseudomonas aeruginosa to invade populations of two
 low-fitness resident clones that differ in their evolvability. Both
 competition from mutations in the resident lineage and environmental
 degradation lead to faster adaptation in the invader through fixing single
 mutations with a greater fitness advantage. The results suggest that
 competition from mutations in both the successful invader and the
 unsuccessful resident shapes the adaptive trajectory of the invader
 through both direct competition and indirect environmental effects.
 Therefore, to predict evolutionary outcomes, it will be necessary to
 consider the evolvability of all members of the community and the effects
 of adaptation on the quality of the environment. This is particularly
 relevant to mixed microbial communities where lineages differ in their
 adaptive potential, a common feature of chronic infections.
description: invader_fitness_in_pristine_envInvader fitness in pristine environment (Figure 2)effect_of_manipulated_env_deg_on_invader_growthEffect of manipulated environmental degradation on invader growth rate (column headings refer to time in 0.5 h increments) (Raw data for Figure 3A)effect_of_evolved_res_on_growth_rateEffect of evolved resident on invader growth rate (column headings refer to time in 0.5 h increments) (Raw data for Figure 3B)effect_of_evolved_res_on_env_degEffect of evolved resident on environmental degradation experienced by invader (computed data for Figure 3B)effect_of_manipulated_env_deg_on_invader_fitnessEffect of manipulated environmental degradation on evolved invader fitness (data for Figure 3C)
DOI: 10.5061/dryad.02674
title: Data from: The ability of Drosophila hybrids to locate food declines with parental divergence.

description: Hybrids between two species are generally less fit than the parental
 species, and the mechanisms underlying their fitness reductions can
 manifest through different traits and at different life history stages.
 For example, hybrids can have physiological, behavioral, or ecological
 defects, resulting in postzygotic isolation between their parental
 species. However, mechanisms of postzygotic isolation other than sterility
 and inviability have remained largely uninvestigated. Isolated studies
 have found that other postzygotic defects are not only possible but might
 be widespread. Here, we study a fundamental animal behavior - the ability
 of individuals to find food - and test the rate at which it breaks down in
 hybrids. We measured the ability of hybrids from 94 pairs of Drosophila
 species to find food and show that hybrids are generally less successful
 than their parental species. We then show that the ability of hybrid
 offspring to locate food decreases with increasing genetic divergence
 between the parental species. Our findings quantify the rate that hybrid
 dysfunction evolves across the diverse radiation of Drosophila and
 highlight the need for future investigations of the genetic and
 neurological mechanisms that affect a hybrid's ability to find a
 suitable substrate on which to feed and breed.
description: hybrid_food_choiceZip file containing raw data as well as scripts used for the analyses. Perl scripts were used to load the data into a MySQL database, and R scripts were used for the analyses and to generate the paper figures.
DOI: 10.5281/zenodo.18384222
title: SuperDARN data in netCDF format (2005-Nov)

description: 2005-Nov SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6633616
title: SuperDARN data in netCDF format (2005-Nov)

description: 2005-Nov SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.mt688
title: Data from: Persistent social interactions beget more pronounced personalities in a desert-dwelling social spider

description: The social niche specialization hypothesis predicts that repeated social
 interactions will generate social niches within groups, thereby promoting
 consistent individual differences in behaviour. Current support for this
 hypothesis is mixed, probably because the importance of social niches is
 dependent upon the ecology of the species. We test whether repeated
 interactions among group mates generate consistent individual differences
 in boldness in the social spider, Stegodyphus dumicola. In support of the
 social niche specialization hypothesis, we found that consistent
 individual differences in boldness increased with longer group tenure.
 Interestingly, these differences took longer to appear than in previous
 work suggesting this species needs more persistent social interactions to
 shape its behaviour. Recently disturbed colonies were shyer than older
 colonies, possibly reflecting differences in predation risk. Our study
 emphasizes the importance of the social environment in generating animal
 personalities, but also suggests that the pattern of personality
 development can depend on subtle differences in species' ecologies.
description: Boldness behavioral
 dataBoldness scores for
 S.dumicola individuals tested in groups of differing familiarity
 levels.Dumicola familiarity
 wide.xlsx
DOI: 10.5061/dryad.p083b
title: Data from: Parasite-mediated selection drives an immunogenetic tradeoff in plains zebras (Equus quagga)

description: Pathogen evasion of the host immune system is a key force driving extreme
 polymorphism in genes of the major histocompatibility complex (MHC).
 Although this gene family is well characterized in structure and function,
 there is still much debate surrounding the mechanisms by which MHC
 diversity is selectively maintained. Many studies have investigated
 relationships between MHC variation and specific pathogens, and have found
 mixed support for and against the hypotheses of heterozygote advantage,
 frequency-dependent or fluctuating selection. Few, however, have focused
 on the selective effects of multiple parasite types on host immunogenetic
 patterns. Here, we examined relationships between variation in the equine
 MHC gene, ELA-DRA, and both gastrointestinal (GI) and ectoparasitism in
 plains zebras (Equus quagga). Specific alleles present at opposing
 population frequencies had antagonistic effects, with rare alleles
 associated with increased GI parasitism and common alleles with increased
 tick burdens. These results support a frequency-dependent mechanism, but
 are also consistent with fluctuating selection. Maladaptive GI parasite
 ‘susceptibility alleles’ were reduced in frequency, suggesting that these
 parasites may play a greater selective role at this locus. Heterozygote
 advantage, in terms of allele mutational divergence, also predicted
 decreased GI parasite burden in genotypes with a common allele. We
 conclude that an immunogenetic trade-off affects resistance/susceptibility
 to parasites in this system. Because GI and ectoparasites do not directly
 interact within hosts, our results uniquely show that antagonistic
 parasite interactions can be indirectly modulated through the host immune
 system. This study highlights the importance of investigating the role of
 multiple parasites in shaping patterns of host immunogenetic variation.
description: Zebra capture
 dataIndividual, season,
 parasite and genetic data from zebras captured in Etosha National Park,
 Nambia.
DOI: 10.5061/dryad.v4g40ms
title: Data from: Protective role of nano-selenium-enriched Bifidobacterium longum in delaying the onset of streptozotocin-induced diabetes

description: Bifidobacterium longum (B. longum) could accumulate Selenium (Se) and
 nano-Se in the form of Se-B. longum and Nano-Se-B. longum, respectively.
 In this study, the effect of Nano-Se-B. longum in diabetic mice was
 evaluated. Physiological and metabolic parameters such as blood glucose,
 body weight, serum insulin level, intraperitoneal glucose tolerance test
 (IPGTT), food intake, water consumption, and urine output were evaluated.
 The expression of insulin signaling pathway-related proteins was evaluated
 by western blotting. Hematoxylin and eosin (H&E) was used for
 histological examination of the liver, pancreas, and kidney sections.
 Creatinine levels in serum (SCr) and blood urea nitrogen (BUN) were
 measured. Nano-Se-B. longum was the best in terms of delaying the onset of
 diabetes. Nano-Se-B. longum decreased blood glucose and body weight
 compared with those noted for the model group. IPGTT, food intake, water
 consumption, and urine output significantly increased and serum insulin
 levels significantly decreased in the model group compared with those in
 all the Nano-Se-B. longum-treated mice. Histological results showed that
 the Nano-Se-B. longum-treated mice were better than the model group mice
 in terms of pathological changes. The expression of insulin signaling
 pathway-related proteins was upregulated in the Nano-Se-B. longum-treated
 groups. A significant increase in SCr and BUN levels was noted in the
 model group. This study for the ﬁrst time reported the dose-dependent
 preventive effect of Nano-Se-B. longum on the onset of diabetes and renal
 damage. The mechanism may be related to changes in insulin signaling.
description: raw
 data-RSOS-181156.R1The files inculde raw
 data of figure 1, figure 2, figure 3, figure 4, and figure 7 in .our
 paper.
DOI: 10.5061/dryad.d76mm
title: Data from: Reproductive allochrony in seasonally sympatric populations maintained by differential response to photoperiod: implications for population divergence and response to climate change

description: Reproductive allochrony presents a potential barrier to gene flow and is
 common in seasonally sympatric migratory and sedentary birds. Mechanisms
 mediating reproductive allochrony can influence population divergence and
 the capacity of populations to respond to environmental change. We asked
 whether reproductive allochrony in seasonally sympatric birds results from
 a difference in response to supplementary or photoperiodic cues and
 whether the response varies in relation to the distance separating
 breeding and wintering locations as measured by stable isotopes. We held
 seasonally sympatric migratory and sedentary male dark-eyed juncos (Junco
 hyemalis) in a common garden in early spring under simulated natural
 changes in photoperiod and made measurements of reproductive and migratory
 physiology. On the same dates and photoperiods, sedentary juncos had
 higher testosterone (initial and gonadotropin-releasing hormone induced),
 more developed cloacal protuberances, and larger testes than migrants. In
 contrast, migratory juncos had larger fat reserves (fuel for migration).
 We found a negative relationship between testis mass and feather hydrogen
 isotope ratios, indicating that testis growth was more delayed in migrants
 making longer migrations. We conclude that reproductive allochrony in
 seasonally sympatric migratory and sedentary birds can result from a
 differential response to photoperiodic cues in a common garden, and as a
 result, gene flow between migrants and residents may be reduced by
 photoperiodic control of reproductive development. Further, earlier
 breeding in response to future climate change may currently be constrained
 by differential response to photoperiodic cues.
description: Am Nat
 dataSpring testosterone,
 corticosterone, fat, cp, gonad mass, and hydrogen isotope data from
 sympatric migrant and resident juncos.