cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.45873cg
title: Data from: Accounting for interspecific competition and age structure in demographic analyses of density dependence improves predictions of fluctuations in population size

description: Understanding species coexistence has long been a major goal of ecology.
 Coexistence theory for two competing species posits that intraspecific
 density dependence should be stronger than interspecific density
 dependence. Great tits and blue tits are two bird species that compete for
 food resources and nesting cavities. Based on long-term monitoring of
 these two competing species at sites across Europe, combining
 observational and manipulative approaches, we show that the strength of
 density regulation is similar for both species, and that individuals have
 contrasting abilities to compete depending on their age. For great tits,
 density regulation is driven mainly by intraspecific competition. In
 contrast, for blue tits, interspecific competition contributes as much as
 intraspecific competition, consistent with asymmetric competition between
 the two species. In addition, including age-specific effects of intra- and
 interspecific competition in density-dependence models improves
 predictions of fluctuations in population size by up to three times.
description: R
 scriptFully annotated R code
 corresponding to 1) the IPM; 2) the 3 density-dependence models shown in
 the paper.Data
 filesFor the 11 sites
 included in the study (see Appendix S1 for a map), for both great tit (GT)
 and blue tit populations (BT), the year of breeding
 "YearOfBreeding", the female identity "MotherID", its
 age "AgeMother", its status "StatusMother"
 ("I" immigrant; "R" locally recruited; "S"
 survived from previous year) and the number of daughters locally recruited
 "NumDaughtersLocal" are provided.
DOI: 10.5061/dryad.2pm2j8j
title: Data from: Ancestral remnants or peripheral segregates? Phylogenetic relationships of two narrowly endemic Euphrasia species (Orobanchaceae) from the eastern European Alps

description: Endemism in mountain ranges is considered to be the result of a number of
 factors, including restriction to refugia during Pleistocene climate
 fluctuations. However, isolation in glacial refugia cannot explain the
 origin of narrowly endemic taxa restricted to formerly heavily glaciated
 areas. Here, we investigate the phylogeny of two narrowly endemic species,
 Euphrasia inopinata and E. sinuata (Orobanchaceae), found exclusively in
 formerly heavily glaciated areas of the eastern European Alps. As both
 species are diploid and very similar to the widespread (allo)polyploid E.
 minima, we test whether the restricted distributions of E. inopinata and
 E. sinuata are relictual, i.e., the two species are ancestral diploid
 remnants of a polyploid complex, or whether they are derived, i.e., the
 two species are peripheral segregates of a more widespread diploid. Based
 on ITS sequence and AFLP fingerprint data it is shown that E. inopinata
 and E. sinuata, whose diploid ploidy level is confirmed for all analysed
 individuals via flow cytometry, are phylogenetically closely related to
 diploid E. alpina s. l. (series Alpinae) instead of E. minima (series
 Parviflorae). In addition, there is no evidence that these two diploid
 species participated in the formation of allotetraploid E. minima. Thus,
 E. inopinata and E. sinuata are interpreted as peripheral segregates of
 the widespread E. alpina s. l.. Shifts in pollination system from allogamy
 in E. alpina s. l. to autogamy in E. inopinata and E. sinuata, genetic
 drift in small populations, and geographic isolation at the periphery of
 the range of E. alpina s. str. probably contributed to the morphological
 and ecological differentiation of E. inopinata and E. sinuata.
description: ITS_alignment_for_mrbayes.nexusNEXUS-formatted ITS alignment for use with MrBayesITS_mrbayes.nexusAFLP_data_matrixFasta-formatted AFLP data matrix. Individual abbreviations as in the Table S1 in the manuscript.
DOI: 10.5061/dryad.tp546d7
title: Data from: Weak spatiotemporal response of prey to predation risk in a freely interacting system

description: 1.The extent to which prey space use actively minimises predation risk
 continues to ignite controversy. Methodological reasons that have hindered
 consensus include inconsistent measurements of predation risk, biased
 spatiotemporal scales at which responses are measured, and lack of robust
 null expectations. 2.We addressed all three challenges in a comprehensive
 analysis of the spatiotemporal responses of adult female elk (Cervus
 elaphus) to the risk of predation by grey wolves (Canis lupus) during
 winter in northern Yellowstone, USA. 3.We quantified spatial overlap
 between the winter home ranges of GPS‐collared elk and three measures of
 predation risk: the intensity of wolf space use, the distribution of
 wolf‐killed elk and vegetation openness. We also assessed whether elk
 varied their use of areas characterised by more or less predation risk
 across hours of the day, and estimated encounter rates between
 simultaneous elk and wolf pack trajectories. We determined whether
 observed values were significantly lower than expected if elk movements
 were random with reference to predation risk using a null model approach.
 4.Although a small proportion of elk did show a tendency to minimise use
 of open vegetation at specific times of the day, overall we highlight a
 notable absence of spatiotemporal response by female elk to the risk of
 predation posed by wolves in northern Yellowstone. 5.Our results suggest
 that predator‐prey interactions may not always result in strong
 spatiotemporal patterns of avoidance.
description: Cusack_et_al_JAE_DataThis zip file contains the data needed to replicate the analyses described in the associated paper. These include elk winter GPS collar data 2012-2016 ("Cusack_et_al_Elk_Data_2012_to_2016.csv"), wolf winter GPS collar data 2004-2016 ("Cusack_et_al_Wolf_data_2004_2016.csv"), elk kill site location data ("Cusack_et_al_Elk_Kill_Site_data.csv"), and a vegetation openness raster layer for northern Yellowstone NP ("Cusack_et_al_Vegetation_Openness.asc")
DOI: 10.5061/dryad.q564pc4
title: Data from: Fibulin-3 has anti-tumorigenic activities in cutaneous squamous cell carcinoma

description: Cutaneous squamous cell carcinoma (cSCC) is the second most common skin
 cancers. Several previous studies have shown that Fibulin-3 participates
 in the occurrence and development of various tumors; however, its role in
 cSCC remains unknown. In the present study, we observed that the
 expression of Fibulin-3 was down-regulated in cSCC tissues compared with
 normal skin tissues, which was due to Fibulin-3 promoter methylation. In
 vitro, knockdown of Fibulin-3 in cSCC cell lines A431 and SCL-1 cells
 promoted cell proliferation, protected cells against apoptosis and
 enhanced the migration and invasion abilities. Conversely, overexpression
 of Fibulin-3 inhibited cell proliferation by promoting growth arrest
 during the G1/S phase transition, induced apoptosis, and reduced the
 migration and invasion abilities. These anticarcinogenic effects of
 Fibulin-3 were associated with inhibition of the AKT signaling pathway.
 Through a mouse xenograft model, we found that Fibulin-3 overexpression
 inhibited the cSCC tumor growth in vivo. Our results suggest that
 Fibulin-3 has anti-tumorigenic activities in cSCC. Down-regulation of
 Fibulin-3 is involved in cSCC development and that it may serve as a novel
 therapeutic target of this disease.
description: photographs of nude
 miceBar
 graphBAR
 graph.rarphotographs of migration
 and invasion assayWestern blotting
 dataWB
 data.rarphotographs of nude mice
 tumor IHCphotographs of cSCC
 tissue IHCphotographs of scc tissue
 IHC.rar
DOI: 10.5061/dryad.6tm7272
title: Data from: Prepared for the future: a strong signal of evolution towards the adult benthic niche during the pelagic stage in Labrid fishes

description: The morphology of organisms reflects a balance between their evolutionary
 history, functional demands, and biomechanical constraints imposed by the
 immediate environment. In many fish species, a marked shift in the
 selection regime is evident when pelagic larvae, which swim and feed in
 the open ocean, settle in their adult benthic habitat. This shift is
 particularly dramatic in coral-reef fishes, where the adult habitat is
 immensely complex. However, whether the adult trophic ecotype affects the
 morphology of early life stages is unclear. We measured a suite of 26
 functional-morphological traits in the head and body of larvae from an
 ontogenetic series of 16 labrid species. Using phylogenetic comparative
 methods, we reconstructed the location of adaptive peaks of larvae whose
 adults are associated with different trophic ecotypes. We found that the
 morphospace occupation in these larvae is largely driven by divergent
 adaptations to the adult benthic habitats. The disparity between adaptive
 peaks is achieved early and does not monotonically increase with size. Our
 findings refute the notion that larvae rapidly acquire the
 trophic-specific traits during a metamorphic period immediately prior to
 settlement. This early specialization might be due to the highly complex
 musculoskeletal system of the head that cannot be rapidly modified.
description: Prepared for the future
 - Raw measurement dataFile containing the raw,
 untransformed measurements of 26 morphological variable. all linear
 measurements (length, width, depth) are in mm. All "surface"
 traits refer to projected areas and are in mm2 (mm squared). The
 assignments to ecotypes is detailed in the supplementary methods (Table
 S3)
DOI: 10.5061/dryad.qp321v7
title: Data from: Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth

description: Administration of sclerostin-neutralizing antibody (Scl-Ab) treatment has
 been shown to elicit an anabolic bone response in growing and adult mice.
 Prior work characterized the response of individual mouse strains but did
 not establish whether the impact of Scl-Ab on whole bone strength would
 vary across different inbred mouse strains. Herein, we tested the
 hypothesis that two inbred mouse strains (A/J and C57BL/6J (B6)) will show
 different whole bone strength outcomes following sclerostin-neutralizing
 antibody (Scl-Ab) treatment during growth (4.5 – 8.5 weeks of age).
 Treated B6 femurs showed a significantly greater stiffness (S) (68.8% vs.
 46.0%) and maximum load (ML) (84.7% vs. 44.8%) compared to A/J. Although
 treated A/J and B6 femurs showed greater cortical area (Ct.Ar) similarly
 relative to their controls (37.7% in A/J and 41.1% in B6), the location of
 new bone deposition responsible for the greater mass differed between
 strains and may explain the greater whole bone strength observed in
 treated B6 mice. A/J femurs showed periosteal expansion and endocortical
 infilling, while B6 femurs showed periosteal expansion. Post-yield
 displacement (PYD) was smaller in treated A/J femurs (-61.2%, p &lt;
 0.001) resulting in greater brittleness compared to controls; an effect
 not present in B6 mice. Inter-strain differences in S, ML, and PYD led to
 divergent changes in work-to-fracture (Work). Work was 27.2% (p = 0.366)
 lower in treated A/J mice and 66.2% (p &lt; 0.001) greater in treated
 B6 mice relative to controls. Our data confirmed the anabolic response to
 Scl-Ab shown by others, and provided evidence suggesting the mechanical
 benefits of Scl-Ab administration may be modulated by genetic background,
 with intrinsic growth patterns of these mice guiding the location of new
 bone deposition. Whether these differential outcomes will persist in adult
 and elderly mice remains to be determined.
description: 8-week-Old AJ and
 C57BL6J Morphologic, Mechanic, and Histomorphometric Raw
 DataPlease see Methods
 section of manuscript for trait abbreviations and measures from which raw
 values were derived.Raw Trait
 Data.xlsx
DOI: 10.5061/dryad.pp68kp4
title: Data from: Sperm duct gland contents increase sperm velocity in the sand goby

description: Sperm performance is often tightly linked to male reproductive success. In
 many demersal gobiid fishes, the male attaches sperm embedded in a mucus
 produced by sperm duct glands, to the nest substrate before spawning takes
 place. Sperm are activated as the mucus and other embedded gland contents
 dissolve into the water. To test the importance of gland content on sperm
 function in Pomatoschistus minutus, a marine fish with external
 fertilization, we used a paired experimental design, with spermatozoa
 tested with and without sperm duct gland contents mixed into seawater. We
 measured sperm velocity, percentage motile sperm and sperm viability over
 time. Sperm were found to swim 7.3% faster when gland contents were mixed
 in the seawater. Percentage motile sperm was unaffected by the gland
 contents. Sperm viability in seawater exceeded 24 h, but was unaffected by
 the gland contents. An increase in sperm velocity of similar magnitude as
 found here has been shown by others to increase reproductive success.
 Since velocity-boosting properties of sperm duct gland contents have now
 been found in three distantly related goby species, these traits may be
 conserved across the Gobiidae family and may aid in reproduction across a
 range of species and environments.
description: CASA
 rawdataComputer assisted sperm
 analysis from Pomatoschistus minutus sperm tested with and without
 associated sperm duct gland substances.Viability
 rawdataSperm viability raw data
 from Pomatoschistus minutus sperm tested with and without associated sperm
 duct gland substances.
DOI: 10.5061/dryad.b78n9r1
title: Data from: The shaping role of self-organization: linking vegetation patterning, plant traits and ecosystem functioning

description: Self-organized spatial patterns are increasingly recognized for their
 contribution to ecosystem functioning, in terms of enhanced productivity,
 ecosystem stability, and species diversity in terrestrial as well as
 marine ecosystems. Most studies on the impact of spatial self-organization
 have focused on systems that exhibit regular patterns. However, there is
 an abundance of patterns in many ecosystems which are not strictly
 regular. Understanding of how these patterns are formed and how they
 affect ecosystem function is crucial for the broad acceptance of
 self-organization as a key-stone process in ecological theory. Here, using
 transplantation experiments in salt-marsh ecosystems dominated by Scirpus
 mariqueter, we demonstrate that scale-dependent feedback is driving
 irregular spatial pattern formation of the vegetation. Field observations
 and experiments revealed that this self-organization process affects a
 range of plant traits (the distributions of orientations, nodes number and
 distances) as well as enhances vegetation productivity, and that
 patchiness in self-organized saltmarsh vegetation can support a better
 micro-habitat for macrobenthos, promoting their total abundance and
 spatial heterogeneity of species richness. Our results extend the existing
 concepts of self-organization and its effects on productivity and
 biodiversity to the spatial irregular patterns that are observed in many
 systems. Our work also helps to link between the so-far largely
 unconnected fields of self-organization theory and trait-based, functional
 ecology.
description: Figure
 2This
 file includes R code and data for the statistical
 analysis.Figure
 3This
 file includes R code and data for the statistical
 analysis.Figure
 4This
 file includes R code and data for the statistical
 analysis.Figure
 5This
 file includes R code and data for the statistical
 analysis.
DOI: 10.34894/c7vbhl
title: Replication Data for: Chimpanzees are not more aggressive than bonobos, but target sexes differently

description: Data and analysis scripts related to the manuscript "Chimpanzees are not more aggressive than bonobos, but target sexes differently" (accepted for publication in Science Advances).
DOI: 10.5061/dryad.17c6c77
title: Data from: Predation risk and resource abundance mediate foraging behaviour and intraspecific resource partitioning among consumers in dominance hierarchies

description: Dominance hierarchies and the resulting unequal resource partitioning
 among individuals are key mechanisms of population regulation. The
 strength of dominance hierarchies can be influenced by size-dependent
 trade-offs between foraging and predator avoidance whereby competitively
 inferior subdominants can access a larger proportion of limiting resources
 by accepting higher predation risk. Foraging-predation risk trade-offs
 also depend on resource abundance. Yet, few studies have manipulated
 predation risk and resource abundance simultaneously; consequently, their
 joint effect on resource partitioning within dominance hierarchies are not
 well understood. We addressed this gap by measuring behavioural responses
 of masu salmon (Oncorhynchus masou ishikawae) to experimental
 manipulations of predation risk and resource abundance in a natural
 temperate forest stream. Responses to predation risk depended on body size
 and social status such that larger fish (often social dominants) exhibited
 more risk-averse behaviour (e.g., lower foraging and appearance rates)
 than smaller subdominants after exposure to a simulated predator. The
 magnitude of this effect was lower when resources were elevated,
 indicating that dominant fish accepted a higher predation risk to forage
 on abundant resources. However, the influence of resource abundance did
 not extend to the population level, where predation risk altered the
 distribution of foraging attempts (a proxy for energy intake) from being
 skewed towards large individuals to being skewed towards small individuals
 after predator exposure. Our results imply that size-dependent
 foraging-predation risk trade-offs can weaken the strength of dominance
 hierarchies by allowing competitively inferior subdominants to access
 resources that would otherwise be monopolized.
description: drift_invertebratesRaw dry mass (g) of drifting invertebrates.Pool_attributesPhysical attributes of pools where experimental manipulations and behavioural observations took place.Drift_collectionDrift net set durations and stream channel attributes used to calculate prey availability in each reach.behaviour dataForaging behaviour of masu salmon before and after exposure to predator stimulus. Abbreviations are the same as those used in the manuscript: FFA is the frequency of foraging attempts when a fish was visible; AR is the appearance rate; AFR is the actual foraging rate (the product of AR and FFA); FA is the total number of foraging attempts.behaviour_data_export.csvAggressive interactionsFrequency of aggressive interactions (AGR) among masu salmon before and after exposure to the predator stimulus.aggressive_interactions.csv
DOI: 10.5061/dryad.qc042n4
title: Data from: Small mammal herbivores mediate the effects of soil nitrogen and invertebrate herbivores on grassland diversity

description: 1. Simultaneous reductions in herbivore abundance and increases in
 nitrogen deposition have led to radical shifts in plant communities
 worldwide. While the individual impacts of these human-caused disturbances
 are apparent, few studies manipulate both herbivory and N, nor
 differentiate among herbivore guilds, to understand contingencies in the
 ability of these drivers to affect producer diversity and productivity. As
 such, understanding how the main and combined effects of increasing soil N
 with declining herbivores may influence plant community structure and
 function is critical to better understand the future of grassland
 ecosystems under multiple global change drivers. 2. In this study, we
 asked: (1) What are the main effects of small mammal herbivores,
 invertebrate herbivores, and soil N on plant community structure and
 function? and (2) Are the effects of invertebrate herbivores and soil N on
 plant community structure and function contingent on small mammal
 herbivory? We used a design, with invertebrate and soil N treatments
 nested within small mammal manipulations in an existing tall grass
 prairie. We quantified plant community structure ( plant richness,
 evenness, diversity, and composition). We also recorded total aboveground
 biomass to quantify grassland productivity. 3. We found that small mammal
 herbivores strongly shaped plant diversity, species composition, and
 productivity. Small mammal herbivores also mediated the effects of soil N
 and invertebrate herbivores on grassland community structure, but not
 composition or productivity. Small mammal reduction lowered plant species
 richness while increasing above ground biomass and altering compositional
 similarity. Invertebrate herbivores, in the presence of small mammals,
 promoted plant dominance by reducing evenness without altering
 compositional similarity. Additionally, soil nitrogen addition reduced
 plant richness, but only when small mammals were reduced, and no effects
 on compositional similarity or productivity. 4. Our findings provide
 further evidence that temperate grasslands productivity and diversity are
 driven by top and bottom up factors.
description: PoeEtAl_PlantCommunity&MicroclimateField data for both 2014 and 2015 growing seasons including plant community and microclimate data. Data were collected at the plot level (1-m in diameter circular plots).