cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tr25v
title: Data from: Consequences of habitat change and resource selection specialization for population limitation in cavity-nesting birds

description: Resource selection specialization may increase vulnerability of
 populations to environmental change. One environmental change that may
 negatively impact some populations is the broad decline of quaking aspen
 Populus tremuloides, a preferred nest tree of cavity-nesting organisms who
 are commonly limited by nest-site availability. However, the long-term
 consequences of this habitat change for cavity-nesting bird populations
 are poorly studied. I counted densities of woody plants and eight
 cavity-nesting bird species over 29 years in 15 high elevation riparian
 drainages in Arizona, USA. I also studied nest tree use and specialization
 over time based on 4946 nests across species. Aspen suffered a severe
 decline in availability over time, while understorey woody plants and
 canopy deciduous trees also declined. The decline of plants resulted from
 increased elk Cervus canadensis browsing linked to declining snowfall.
 Woodpeckers exhibited very high specialization (&gt;95% of nests) on
 aspen for nesting, and densities of all six species declined with aspen
 over time. Mountain chickadees Poecile gambeli and house wrens Troglodytes
 aedon exhibited increasingly less specialization on aspen. Chickadees
 strongly increased in density over time, despite a relatively high
 specialization on aspen. House wren densities declined moderately over
 time, but nest box addition experiments demonstrated that nest-site
 availability was not limiting their population. House wren densities
 increased with understorey vegetation recovery in elk exclosures via
 increased generality of nest site use, demonstrating that the decline in
 understorey vegetation on the broader landscape was the cause of their
 population decline. Synthesis and applications. Management should target
 species that specialize in resource selection on a declining resource.
 Species with greater resource selection generalization can reduce
 population impacts of environmental change. Resource generalization can
 allow a species like the wren to take advantage of habitat refuges, such
 as those provided by the elk exclosures. Yet, resource generalization
 cannot offset the negative impacts of broad-scale declines in habitat
 quality on the landscape, as demonstrated by the general decline of wrens.
 Ultimately, aspen is an important habitat for biodiversity, and land
 management programs that protect and aid recovery of aspen habitats may be
 critical.
description: FielddataField data
DOI: 10.5061/dryad.v704dj2
title: Data from: Hydrological niche segregation defines forest structure and drought tolerance strategies in a seasonal Amazon forest

description: 1) Understanding if and how trees coordinate rooting depth and aboveground
 hydraulic traits to define drought-resistance strategies in seasonal
 Amazon forests is a major gap to model parametrization aimed at predicting
 the effects of climate change in these ecosystems. 2) We assessed the
 rooting depth of 12 dominant tree species (representing ~ 42% of the
 forest basal area) in a seasonal Amazon forest, using the stable isotope
 ratios (δ18O and δ²H) of water collected from tree xylem and soils from a
 range of depths. We took advantage of a major ENSO-related drought in
 2015/2016 that caused substantial evaporative isotope enrichment on soil.
 We measured the minimum dry-season leaf water potential both in a normal
 year (2014; Ψnon-ENSO) and in an extreme drought year (2015; ΨENSO).
 Furthermore, we measured xylem hydraulic traits that indicate the range of
 water potentials that trees tolerate without risking hydraulic failure
 (P50 and P88). 3) We demonstrate that coexisting trees are largely
 segregated along a single hydrological niche axis defined by root depth
 differences, access to light, and tolerance of low water potential. These
 differences in rooting depth were strongly related to tree size; diameter
 at breast height (DBH) explained 72% of the variation in the δ18Oxylem.
 Additionally, δ18Oxylem explained 49% of the variation in P50 and 70% of
 P88, with higher tolerance of low water potential in shallow-rooted
 species, while δ18O of xylem water explained 47% and 77% of the variation
 of minimum Ψnon-ENSO and ΨENSO. 4) We propose a new formulation to
 estimate an effective functional rooting depth, i.e., the likely soil
 depth from which roots can sustain water uptake for physiological
 functions, using DBH as predictor of root depth at this site. Based on
 these estimates, we conclude that a number of families, genera and species
 are restricted to drawing water from shallow to deep soil in a large area
 of the Tapajós forest. 5) Our results support the theory of hydrological
 niche segregation and its underlying trade-off related to drought
 resistance, which also affect the dominance structure of trees in this
 seasonal eastern Amazon forest.
description: Brum_et_al_2018_JoE
DOI: 10.5061/dryad.gh761
title: Data from: Predation risk affects growth and reproduction of an invasive snail and its lethal effect depends on prey size

description: The behavior of invasive species under predation risk has been studied
 extensively, but their growth and reproductive responses have rarely been
 investigated. We conducted experiments with juveniles and adults of the
 invasive freshwater snail Pomacea canaliculata, and we observed changes in
 growth and reproduction in response to predation risk from a caged
 predator (Trachemys scripta elegans). P. canaliculata produced eggs
 earlier in the presence of predators and injured conspecifics compared
 with the control group (no risk), although the total number of egg masses
 laid by per female was exceeded by that of the controls after 15 days. Egg
 hatching success noticeably decreased under predation risk, and the
 incubation period was significantly prolonged; however, the oviposition
 height of the snails was not affected. A lethal effect of predation risk
 was detected in juvenile snails but not in adults. The growth of juvenile
 P. canaliculata was inhibited under predation risk, probably due to a
 reduction in food intake. Adult females exhibited a greater reduction in
 growth under predation risk than males, which likely resulted in part from
 the high reproductive investment of females in egg laying. These results
 indicate that P. canaliculata snails under predation risk face a trade-off
 between predator avoidance and growth and reproduction, where the lethal
 effect of predation risk is linked to the size of the prey.
description: Growth and reproduction
 of Pomacea canaliculataThe file provides
 information about survival, growth, food intake, egg mass production,
 clutch size, oviposition height, hatching success and incubation period of
 an invasive snail Pomacea canaliculata under predation
 risk.
DOI: 10.5061/dryad.69v95
title: Data from: Influenza A virus: sampling of the unique shorebird habitat at Delaware Bay, USA

description: Delaware (DE) Bay, in the northeastern United States, has long been
 recognized as a hotspot for avian influenza A virus (IAV); every spring,
 this coastal region serves as a brief stopover site for thousands of
 long-distance migrating shorebirds, en route to breeding grounds in the
 Arctic. During these stopovers, IAV have been consistently recovered from
 Ruddy Turnstones (Arenaria interpres) that are likely to become infected
 as they feed by probing sand and cobble in search of food. In May 2010 –
 2012, we successfully isolated 19 IAV from environmental samples (sand, n
 = 18; horseshoe crab eggs, n = 1) obtained from DE Bay sites. Two of these
 viruses were subjected to laboratory conditions similar to those in the DE
 Bay spring-time environment, and remained infectious for seven days. Here,
 through the recovery of IAV from environmental samples, temperature
 monitoring at and below the sand surface, and simulated laboratory trials,
 we provide evidence that the beach environment may enable localized
 transmission and short-term maintenance of IAV in this unique ecosystem.
description: Poulson_supplemental
 data file_persistence
DOI: 10.5061/dryad.s08f7
title: Data from: Can above-ground ecosystem services compensate for reduced fertilizer input and soil organic matter in annual crops?

description: Above-ground and below-ground environmental conditions influence crop
 yield by pollination, pest pressure, and resource supply. However, little
 is known about how interactions between these factors contribute to yield.
 Here, we used oilseed rape Brassica napus to test their effects on crop
 yield. We exposed potted plants to all combinations of high and low levels
 of soil organic matter (SOM) and fertilizer supply, and placed all
 treatments at a variety of field sites representing a gradient in
 pollinator visitation rate and pest exposure. We determined the relative
 contribution of pollinators and pests, SOM and fertilizer supply to yield.
 We also tested whether SOM can moderate effects of fertilizer on yield and
 whether soil conditions influence the relationship between above-ground
 conditions and yield. Increases in pollinator visitation rate and
 decreases in pest pressure enhanced yield more than increase of fertilizer
 supply. Although higher SOM content resulted in plants with more biomass
 and flowers, under our experimental conditions SOM neither enhanced yield,
 nor influenced effects of fertilizer, pollinators or pests on yield. The
 relationships between yield, pollinator visitation rate and pest pressure
 did not depend on the level of fertilization suggesting that the effects
 of fertilizer application and above-ground (dis)services on yield were
 additive. In contrast, pollinator visitation rate was more strongly
 related to yield at low pest pressure than at high pest pressure
 indicating trade-offs between above-ground services and disservices.
 Synthesis and applications. Our results show that it is possible to
 increase oilseed rape yield by enhancing pollination, irrespective of
 supplying mineral fertilizer. Moreover, the fact that below-ground
 conditions did not alter the effect of above-ground conditions, suggests
 that farmers may obtain even higher yields by maximizing both above-ground
 ecosystem services and external inputs. Further studies are needed to
 understand at which point the positive relationships between pollinator
 visitation and yield, as well as between fertilizer and yield will level
 off. Considering above-ground and below-ground services and inputs in
 agro-ecosystems in conjunction is crucial in order to optimize external
 inputs for crop yield from an economic and ecological perspective.
description: Data van Gils et al.
 2016Data collected in the
 field. See ReadMe file for information about used
 abbreviations.
DOI: 10.5061/dryad.250dt
title: Data from: Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution

description: In mammals, gamete production is essential for reproductive success. This
 is particularly true for males where large quantities of sperm are
 produced to fertilize a limited number of eggs released by the female.
 Because of this, new genes associated with increased spermatogenic
 efficiency have been accumulating throughout the evolution of therian
 mammals. Many of these new genes are testis-specific retrotransposed
 copies of housekeeping genes located on the X chromosome. Of particular
 interest are retrotransposed copies of UTP14 that are present in many
 distantly related eutherian mammals. Analysis of genomic data available in
 ENSEMBL indicates that these UTP14 retrogenes have arisen independently in
 the various eutherian clades. They represent an interesting aspect of
 evolution whereby new homologues of UTP14 have become independently fixed
 in multiple mammalian lineages due to the reproductive advantage that may
 be conferred to males. Surprisingly, these genes may also be lost, even
 after being present within a lineage for millions of years. This
 phenomenon may potentially be used to delineate evolutionary trees in
 closely related groups of mammals, particularly in the case of South
 American primates. Studying these retrogenes will yield new insights into
 the evolutionary history of male gamete production and the phylogeny of
 eutherian mammals.
description: UTP14a transcript
 sequence and UTP14 peptide sequence use.Human UTP14a sequence
 data used for BLAST search of ENSEMBL species specific genome data ti
 identify UTP14 retrogenes. Primate UTP14a and UTP14 retrogene encoded
 peptide sequences used to generate phylogeny trees.Combined
 RawDataRSOS.docx
DOI: 10.5061/dryad.p71fk
title: Data from: A new pliosaurid (Sauropterygia, Plesiosauria) from the Oxford Clay Formation (Middle Jurassic, Callovian) of England: evidence for a gracile, longirostrine grade of Early–Middle Jurassic pliosaurids

description: A partial skeleton from the Sigiloceras enodatum ammonite Subzone (early
 Callovian, Middle Jurassic) of the Oxford Clay Formation of Quest Pit,
 near Stewartby, Bedfordshire, UK respresents one of the basalmost Middle
 Jurassic pliosaurids. Marmornectes candrewi gen. et sp. nov. possesses
 seven autapomorphies and a longirostrine snout. Reassessment of
 pliosauroid relationships demonstrates that Thalassiodracon hawkinsii,
 Hauffiosaurus spp. and Attenborosaurus conybeari are successively more
 derived basal representatives of Pliosauridae. This indicates that a
 longirostrine snout was acquired among Early Jurassic pliosaurids (such as
 Hauffiosaurus), but that these early taxa had a small body size, long
 neck, and gracile skull and limb bones relative to the contemporaneous
 rhomaleosaurids, which were robust, large-bodied macropredators. The
 pliosaurid lineage only acquired its ‘characteristic’ large size, robust
 skull and short neck in the late Middle Jurassic after the extinction of
 Rhomaleosauridae.
description: Ketchum_&_Benson_data_files
DOI: 10.5061/dryad.tv210
title: Data from: Dark pigmentation limits thermal niche position in birds

description: 1. Animal pigmentation has evolved because of several adaptive functions.
 In the case of pigmentation produced by melanins, the most common pigments
 in animals, the main function is protection against UV radiation. However,
 pigmentation also affects animal surface's ability to absorb solar
 radiation and gain heat, which may represent a thermal constraint for
 endotherms due to their relatively high and constant body temperatures. 2.
 As darker colours absorb more radiation than lighter colours,
 dark-pigmented endotherm animals may exhibit limited performance under
 high ambient temperatures and thus be constrained at occupying hot
 environments. While the influence of pigmentation on the determination of
 the thermal niches of ectotherms, particularly reptiles, has been the
 focus of several studies, this remains an unexplored issue for endotherm
 animals. 3. Here we made a detailed quantification of the expression of
 pigmentation phenotypes produced by melanins in 96 species of birds
 inhabiting the Spanish sector of the Iberian Peninsula and estimated their
 climate niche position by calculating the effects of ambient temperature,
 insolation and precipitation on bird occurrence at a fine 10 x 10 km
 spatial scale. 4. After controlling for the body size and the nocturnal
 condition of species, and for phylogenetic and spatial effects, we found a
 positive association between plumage reflectance and the functional
 response of bird distribution to spring-summer ambient temperature and
 insolation but not to precipitation. Thus, bird species preferentially
 occupying the hotter and sunnier areas of Spain exhibit lighter plumage
 pigmentation. A similar association between pigmentation and preferences
 regarding precipitation in geographical distribution was not found. 5. Our
 findings suggest that darker birds are limited to occupying environments
 with high temperatures, unveiling a constraint in endotherms imposed by
 their pigmentation phenotype.
description: Database used in the
 studyPigmentation radiation - Dryad
 data.xlsx
DOI: 10.5061/dryad.s6j3678
title: Data from: Risk taking of educated nematodes

description: Nematode parasites rely on successful host infection to perpetuate their
 species. Infection by individual nematode parasites can be risky, however;
 any one individual could be killed by the host's immune response.
 Here we use a model system to show that environmental cues and parasite
 past experience can be used by entomopathogenic nematodes to reduce
 individual risk of infection. Past parasite experience can more than
 double the infective virulence (number of host invaders) of a given cohort
 of entomopathogenic nematode parasites. This plasticity in individual
 parasite risk-taking and associated infection can be used to manage
 infection of parasitic nematodes: enhancing biological control with
 entomopathogenic nematodes and developing behavioral and chemical
 strategies to reduce infection by vertebrate and plant parasitic
 nematodes.
description: willett_etal_2018Results from entomopathogenic nematode bioassays.
DOI: 10.5061/dryad.524gv
title: Data from: Environmental complexity influences association network structure and network-based diffusion of foraging information in fish shoals

description: Socially transmitted information can significantly affect the ways in
 which animals interact with their environments. We used network-based
 diffusion analysis, a novel and powerful tool for exploring information
 transmission, to model the rate at which sticklebacks (Gasterosteus
 aculeatus) discovered prey patches, comparing shoals foraging in open and
 structured environments. We found that for groups in the open environment,
 individuals tended to recruit to both the prey patch and empty comparison
 patches at similar times, suggesting that patch discovery was not greatly
 affected by direct social transmission. In contrast, in structured
 environments we found strong evidence that information about prey patch
 location was socially transmitted and moreover that the pathway of
 information transmission followed the shoals’ association network
 structures. Our findings highlight the importance of considering habitat
 structure when investigating the diffusion of information through
 populations and imply that association networks take on greater ecological
 significance in structured than open environments.
description: Webster et al. NBDA_Am
 NatPart 1: Association
 matrices used to compare association network structure in open and
 structured environments.Part 2a: Association matrices used to compare
 association network structure in open and structured environments for
 diffusion analysis. Part 2b: Prey and control patch entry times and
 orders, used in diffusion analysis.
DOI: 10.5061/dryad.53p48
title: Data from: How do different aspects of biodiversity change through time? A case study on an Australian bird community

description: The study of ecological communities through time can reveal fundamental
 ecological processes and is key to understanding how natural and human
 pressures will affect biodiversity. Most studies of ecological communities
 through time consider only one or a few summary measures (e.g. species
 richness, total abundance), which might neglect important aspects of
 community structure or function. We studied temporal variation in several
 measures of species diversity, size diversity, and species composition in
 an intensively sampled bird community to determine whether different
 biodiversity measures change synchronously. We used a novel function
 regression model, which supports the study of diversity measures that are
 distributions (e.g. species abundance distributions) alongside measures
 that are scalar values (e.g. species richness). Most diversity measures
 changed predictably within years, but inter-annual changes in size
 diversity and species composition were not reflected in species diversity.
 Within and among years, there was considerable variation in distributional
 measures that was not captured in scalar measures. Predictable variation
 within years probably was related to seasonal variation in weather
 patterns or food availability, but variation in size diversity among years
 probably resulted from stochastic changes in species composition. These
 results suggest that species and size diversity may be decoupled, and that
 inferences on scalar diversity measures might not reflect fundamental
 changes to community structure or function. Our method supports the
 inclusion of size-based measures and distributional measures in ecological
 analyses, and broader uptake of our approach is likely to provide new
 insight into the processes structuring ecological communities, and inform
 the links between structure and function in ecological communities.
description: Bird community data
 through time in an Australian forestSummary diversity
 indices, species abundance distributions, individual size distributions,
 and rank abundance spectra for 92 surveys at three locations in Olinda
 State Forest from July 1993 to June 1996. Each survey was a 2 h transect
 traversal starting at sunrise on a given survey day. Body mass data were
 estimated using a simulation approach.data-files.zip
DOI: 10.5061/dryad.hq1hr
title: Data from: Estimating species colonization dates using DNA in lake sediment

description: 1. Detection of DNA in lake sediments holds promise as a tool to study
 processes like extinction, colonization, adaptation and evolutionary
 divergence. However, low concentrations make sediment DNA difficult to
 detect, leading to high false negative rates. Additionally, contamination
 could potentially lead to high false positive rates. Careful laboratory
 procedures can reduce false positive and negative rates, but should not be
 assumed to completely eliminate them. Therefore, methods are needed that
 identify potential false positive and negative results, and use this
 information to judge the plausibility of different interpretations of DNA
 data from natural archives. 2. We developed a Bayesian algorithm to infer
 the colonization history of a species using records of DNA from
 lake-sediment cores, explicitly labelling some observations as false
 positive or false negative. We illustrate the method by analysing DNA of
 whitefish (Coregonus lavaretus. L) from sediment cores covering the past
 10,000 years from two central Swedish lakes. We provide the algorithm as
 an R-script, and the data from this study as example input files. 3. In
 one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea
 and the degree of whitefish ecotype differentiation suggested colonization
 immediately after deglaciation, DNA was indeed successfully recovered and
 amplified throughout the postglacial sediment. For this lake we found no
 loss of detection probability over time, but a high false negative rate.
 In the other lake, Hotagen, where connectivity and ecotype differentiation
 suggested colonization long after deglaciation, DNA was amplified only in
 the upper part of the sediment, and colonization was estimated at 2,200 BP
 based on the assumption that successful amplicons represent whitefish
 presence. Here the earliest amplification represents a false positive with
 a posterior probability of 41%, which increases the uncertainty in the
 estimated time of colonization. 4. Complementing careful laboratory
 procedures aimed at preventing contamination, our method estimates
 contamination rates from the data. By combining these results with
 estimates of false negative rates, our models facilitate unbiased
 interpretation of data from natural DNA archives.
description: HotagenCarbon 14 data from lake Hotagen.LogdasjonCarbon 14 data from lake Stora Lögdasjön.Hotagen_DNAPrimer amplification data from lake Hotagen.Logdasjon_DNAPrimer amplification data from lake Stora Lögdasjön.SedimentDNA_MIModel 1 R script.SedimentDNA_MIIModel 2 R script.SedimentDNA_MIIIModel 3 R script.