cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cm7r1q2
title: Data from: Enhancing insights into foraging specialization in the world’s largest fish using a multi-tissue, multi-isotope approach

description: Intra-species variability in foraging strategies may be common, which has
 significant implications for efforts to understand and manage enigmatic
 species like the whale shark Rhincodon typus. The ecological relevance of
 differences in tissue isotopes within and between individuals in the
 context of foraging however depends on understanding tissue turnover times
 and carbon (Δ13C) and nitrogen (Δ15N) discrimination, which can vary with
 physiology, metabolism and diet quality. Here we examine isotope dynamics
 in captive R. typus as a basis for enhanced ecological insights into wild
 populations of the world’s largest fish and other enigmatic species. A
 variable diet, principally consisting of two krill (Euphausia pacifica and
 E. superba) provided an average of 48 MJ d-1 (± 20 S.D.), or 2.7 times (±
 1.3) basal metabolic requirements. On this diet, in agreement with
 allometric relationships, large body sizes (3,000 to 4,000 kg) were
 matched by slow plasma and cartilage turnover rates (empirically derived
 as 9 months and 3 years, respectively), which provide tissue-specific
 limits on the time-scales over which we can isotopically detect changes in
 diet in this species. Average diet-to-tissue discrimination showed
 significant variation between tissues (plasma and cartilage), and among
 growing and fasting individuals (Δ13C range: 1.5 – 5.5 ‰; Δ15N range: −0.1
 – 2.9 ‰). Assimilation rates increased with temperature and were higher
 for the smaller E. pacifica (15 ± 2 mm) than E. superba (48 ± 2 mm).
 Growth significantly lowered both Δ15Nplasma and Δ15Ncartilage, with
 inappetence markedly reducing Δ15Nplasma and Δ13Cplasma, as well as
 significantly altering blood biochemistry. Captive findings facilitated
 the first robust multi-tissue growth- and nutrition-corrected isotope
 analysis of a wild R. typus population, suggesting individual foraging
 specialization on low trophic level mid-ocean or coastal prey. Long-term
 fasting during ocean-basin scale migrations may be common and such
 metabolic effects should be carefully quantified when isotopically
 assessing intra-species foraging differences. The
 metabolically-constrained multi-tissue, multi-isotope approach described
 can facilitate ecological insights that are indispensable for effective
 conservation and management of globally threatened, but poorly understood,
 species by identifying differences in key foraging areas and target prey
 within and between individuals.
description: Wyatt et
 al_2018_TissueIsotopesTissue stable isotope
 and radiocarbon analyses of captive whale sharks, their feed, and wild
 whale sharksWyatt et
 al_2018_CSIA-AATissue compound specific
 isotope analysis of individual amino acids (CSIA-AA) from captive whales
 sharks, their feed, and wild whale sharksWyatt et
 al_2018_FeedingDaily feeding data from
 captive whale sharks in kg
DOI: 10.5061/dryad.v1v7856
title: Data from: The biogeographical patterns of species richness and abundance distribution in stream diatoms are driven by climate and water chemistry

description: In this inter-continental study of stream diatoms, we asked three
 important but still unresolved ecological questions: 1) What factors drive
 the biogeography of species richness and species abundance distribution
 (SAD); 2) Are climate-related hypotheses, which have dominated the
 research on the latitudinal and altitudinal diversity gradients, adequate
 in explaining spatial biotic variability; and 3) Is the SAD response to
 the environment independent of richness? We tested a number of climatic
 theories and hypotheses (i.e., the species-energy and the metabolic
 theory; and the energy variability and the climatic tolerance hypothesis)
 but found no support for any of these concepts as the relationships of
 richness with explanatory variables were non-existent, weak or unexpected.
 Instead, we demonstrated that diatom richness and SAD evenness generally
 increased with temperature seasonality and at mid- to high total
 phosphorus concentrations. The spatial patterns of diatom richness and the
 SAD—mainly longitudinal in the US, but latitudinal in Finland—were defined
 primarily by the covariance of climate and water chemistry with space. The
 SAD was not entirely controlled by richness, emphasizing its utility for
 ecological research. Thus, we found support for the operation of both
 climate and water chemistry mechanisms in structuring diatom communities,
 which underscores their complex response to the environment and the
 necessity for novel predictive frameworks.
description: Stream spatial,
 environmental, and diatom data from the US and FinlandData are compiled in an
 Excel spreadsheet with 4 tabs containing the following information: 1) US
 community data: spatial, environmental, and diatom community data for 526
 stream sites in the US; 2) US species data: species abundance (diatom cell
 counts and density) for each of the 526 stream sites in the US; 3) Finnish
 community data: spatial, environmental, and diatom community data for 100
 stream sites in Finland; 4) Finnish species data: species abundance
 (diatom cell counts) for each of the 100 stream sites in
 Finland.Passy et al Am Nat
 2018.xlsx
DOI: 10.5061/dryad.8nv72
title: Data from: Individual variation in cone photoreceptor density in house sparrows: implications for between-individual differences in visual resolution and chromatic contrast

description: Between-individual variation has been documented in a wide variety of
 taxa, especially for behavioral characteristics; however, intra-population
 variation in sensory systems has not received similar attention in wild
 animals. We measured a key trait of the visual system, the density of
 retinal cone photoreceptors, in a wild population of house sparrows
 (Passer domesticus). We tested whether individuals differed from each
 other in cone densities given within-individual variation across the
 retina and across eyes. We further tested whether the existing variation
 could lead to individual differences in two aspects of perception: visual
 resolution and chromatic contrast. We found consistent between-individual
 variation in the densities of all five types of avian cones, involved in
 chromatic and achromatic vision. Using perceptual modeling, we found that
 this degree of variation translated into significant between-individual
 differences in visual resolution and the chromatic contrast of a plumage
 signal that has been associated with mate choice and agonistic
 interactions. However, there was no evidence for a relationship between
 individual visual resolution and chromatic contrast. The implication is
 that some birds may have the sensory potential to perform “better” in
 certain visual tasks, but not necessarily in both resolution and contrast
 simultaneously. Overall, our findings (a) highlight the need to consider
 multiple individuals when characterizing sensory traits of a species, and
 (b) provide some mechanistic basis for between-individual variation in
 different behaviors (i.e., animal personalities) and for testing the
 predictions of several widely accepted hypotheses (e.g., honest
 signaling).
description: Cell counts,
 proportions, and spatial resolving power by siteThis file contains the
 raw data of cell counts and proportions by site, and all other fixed
 effects that were included in the models of cell densities and
 proportions. It also includes the spatial resolving power values estimated
 per site.Chromatic
 contrastsThis file contains the
 chromatic contrasts calculated for each retina, for each wingbar exemplar.
 Please see Appendix S2 for details on these calculations. These were the
 data used in statistical models of individual variation in chromatic
 contrasts.
DOI: 10.5061/dryad.17qs8
title: Data from: How to escape from crop-to-weed gene flow: phenological variation and isolation-by-time within weedy sunflower populations

description: The evolution of crop-related weeds may be constrained by recurrent gene
 flow from the crop. However, flowering time variation within weedy
 populations may open the way for weed adaptation by allowing some weeds to
 escape from this constraint. We investigated this link between phenology,
 gene flow and adaptation in weedy sunflower populations recently emerged
 in Europe from crop-wild hybridization. We studied jointly flowering
 phenology and genetic diversity for 15 microsatellite loci in six
 cultivated sunflower fields infested by weedy sunflower populations. The
 flowering overlap of cultivated and weedy sunflowers varied between and
 within populations: some weedy individuals were found completely isolated
 from the crop, the frequency of these plants being higher in populations
 from highly infested fields. Within weedy populations, we detected a
 pattern of isolation-by-time: the genetic divergence between individuals
 was positively correlated with their divergence in flowering period.
 Additionally, earlier weeds, which flowered synchronously with the crop,
 were genetically more similar to the cultivated varieties than
 late-flowering weeds. Overall our results suggest that crop-to-weed gene
 flow did occur but was limited by divergent phenologies. We discuss the
 roles of weed adaptation and population history in generating this partial
 reproductive isolation.
description: Genetypic_dataGenotypic data for 15 microsatellites for weedy individuals and 24 varieties; missing data coded as NAPhenotypic_dataThe Excel file has both the data (one worksheet per weedy population, one worksheet for phenological data of cultivated fields), and a worksheet explaining each of the columns/fields.
DOI: 10.5061/dryad.h2372g0
title: Data from: A continuous model of physiological prion aggregation suggests a role for Orb2 in gating long-term synaptic information

description: The regulation of mRNA translation at the level of the synapse is believed
 to be fundamental in memory and learning at cellular level. The family of
 Cytoplasmic Polyadenylation Element Binding (CPEB) proteins emerged as an
 important RNA binding protein family during development and in adult
 neurons. Drosophila Orb2 (homolog of mouse CPEB3 protein and of the neural
 isoform of Aplysia CPEB) has been found to be involved in the translation
 of plasticity-dependent mRNAs and has been associated to Long Term Memory.
 Orb2 protein presents two main isoforms, Orb2A and Orb2B, which form an
 activity induced amyloid-like functional aggregate, that is thought to be
 the translation-inducing state of the RNA binding protein. Here we present
 a first two-states continuous differential model for Orb2A-Orb2B
 aggregation. This model provides new working hypotheses for studying the
 role of prion-like CPEB proteins in long term synaptic plasticity.
 Moreover, this model can be used as a first step to integrate translation-
 and protein aggregation-dependent phenomena in synaptic facilitation
 rules.
description: Supplementary File
 1This
 is a Python 3.5 script of the ODE model described in Sanguanini and
 Cattaneo 2018. This file contains a model which uses only one stimulation
 pattern and was used to generate Figure 2.SupplementaryFile1.pySupplementary File 2This is a Python 3.5 script of the ODE model described in Sanguanini and Cattaneo 2018. This file contains a model which uses two stimulation patterns and it has been used to generate Figure 3.SupplementaryFile2.pySupplementary File 3This is a Python 3.5 script of the ODE model described in Sanguanini and Cattaneo 2018. This file evaluates the resting-state output of the model for multiple values of \beta_{self} e \beta_+ and was used to generate Figure 4 panels C1 and C2.SupplementaryFile3.pyFigure 5 dataSource data for Figure 5.Fig5_source.txtFigure 4C DataSource file for Figure 4 panel C.Fig4C_source.csvFigure 4A dataSource file Figure 4 panel AFig4A_source.txtFigure 4B DataSource file Figure 4 panel B.Fig4B_source.txtFigure 2A dataSource file for Figure 2 panel A.Fig2A_source.txtFigure 2B dataSource file Figure 2 panel B.Fig2B_source.txtFigure 2C dataSource file for Figure 2 panel C.Fig2C_source.txtFigure 2D dataSource file for Figure 2 panel D.Fig2D_source.txtFigure 3 dataSource file for Figure 3.Fig3_source.txt
DOI: 10.5061/dryad.g9v97vq
title: Data from: Temperature shapes the costs, benefits, and geographic diversification of sexual coloration in a dragonfly

description: The environment shapes the evolution of secondary sexual traits by
 determining how their costs and benefits vary across the landscape. Given
 the thermal properties of dark coloration generally, temperature should
 crucially influence the costs, benefits, and geographic diversification of
 many secondary sexual color patterns. We tested this hypothesis using
 sexually selected wing coloration in a dragonfly. We find that greater
 wing coloration heats males—the magnitude of which improves flight
 performance under cool conditions but dramatically reduces it under warm
 conditions. In a colder region of the species’ range, behavioral
 observations of a wild population show that these thermal effects
 translate into greater territorial acquisition on thermally variable days.
 Finally, geo-referenced photographs taken by citizen scientists reveal
 that this sexually selected wing coloration is dramatically reduced in the
 hottest portions of the species’ range. Collectively, our results
 underscore temperature’s capacity to promote and constrain the evolution
 of sexual coloration.
description: Moore_et_al_ELE_heating_coef_naturalMoore_et_al_ELE_heating_coef_manipMoore_et_al_ELE_weight_liftingMoore_et_al_ELE_territory_acquisitionMoore_et_al_ELE_territory_tenuresMoore_et_al_ELE_geo_varMoore_et_al_ELE_WingColor_Thx.ColorMoore_et_al_ELE_mass_WingColor_comparison
DOI: 10.34740/kaggle/dsv/14631276
title: Berita UNDIP
DOI: 10.5061/dryad.4t53n
title: Data from: Historical amphibian declines and extinctions in Brazil linked to chytridiomycosis

description: The recent increase in emerging fungal diseases is causing unprecedented
 threats to biodiversity. The origin of spread of the frog-killing fungus
 Batrachochytrium dendrobatidis (Bd) is a matter of continued debate. To
 date, the historical amphibian declines in Brazil could not be attributed
 to chytridiomycosis; the high diversity of hosts coupled with the presence
 of several Bd lineages predating the reported declines raised the
 hypothesis that a hypervirulent Bd genotype spread from Brazil to other
 continents causing the recent global amphibian crisis. We tested for a
 spatio-temporal overlap between Bd and areas of historical amphibian
 population declines and extinctions in Brazil. A spatio-temporal
 convergence between Bd and declines would support the hypothesis that
 Brazilian amphibians were not adapted to Bd prior to the reported
 declines, thus weakening the hypothesis that Brazil was the global origin
 of Bd emergence. Alternatively, a lack of spatio-temporal association
 between Bd and frog declines would indicate an evolution of host
 resistance in Brazilian frogs predating Bd's global emergence,
 further supporting Brazil as the potential origin of the Bd panzootic.
 Here, we Bd-screened over 30 000 museum-preserved tadpoles collected in
 Brazil between 1930 and 2015 and overlaid spatio-temporal Bd data with
 areas of historical amphibian declines. We detected an increase in the
 proportion of Bd-infected tadpoles during the peak of amphibian declines
 (1979–1987). We also found that clusters of Bd-positive samples
 spatio-temporally overlapped with most records of amphibian declines in
 Brazil's Atlantic Forest. Our findings indicate that Brazil is post
 epizootic for chytridiomycosis and provide another piece to the puzzle to
 explain the origin of Bd globally.
description: Full database on
 Brazilian tadpolesPresence of Bd infection
 in tadpoles from BrazilFull_Database_Bd_Brazil_CarvalhoBeckerToledo.xls
DOI: 10.5061/dryad.6qm33c6
title: Data from: Intersexual 'arms race' and the evolution of the sphragis in Pteronymia butterflies

description: Sexual reproduction is often associated with intra- and intersexual
 conflict, especially in species where females mate multiple times. A
 strategy that has evolved in males to ensure offspring paternity is the
 ability to produce a complex, external mating plug called a sphragis. The
 sphragis has been found in 273 butterfly species; however, little is known
 about the sphragides of the butterflies in the nymphalid genus Pteronymia.
 In this study, we describe the sphragides of all sphragis-bearing species
 in Pteronymia, including the newly discovered sphragides of P. alissa
 (Hewitson), P. andreas (Weeks), P. ozia (Hewitson), and P. zerlina
 (Hewitson). Three additional species, P. fulvimargo Butler &
 Druce, P. oneida (Hewitson), and P. ticida (Hewitson), are found to bear
 an irregular sphragis-like structure. We use molecular and morphological
 data from a recent study to construct a phylogeny of species in the genus
 and examine the number of independent origins of the sphragis. Our
 ancestral state reconstruction using Bayesian inference suggests that the
 sphragis evolved three times in Pteronymia, whereas parsimony character
 optimization performed on a maximum likelihood tree suggests only one
 origin of this structure. Our data on ancestral state patterns, frequency
 of incomplete sphragides, and morphology of female external genitalia
 suggest that sphragis-bearing Pteronymia may be in active intersexual
 conflict, where females develop strategies to prevent male plugging.
description: Concatenated sequence
 alignmentThis is data from
 De-Silva et al. 2017, which has been concatenated and trimmed for this
 study. These alignments were used in both Bayesian and Maximum Likelihood
 analyses.alignment.nexML tree (molecular and morphology data)Tree file resulting from ML analysis with a dataset that includes molecular and morphology data from De-Silva et al. 2017.mol_morph_iqtree.treBI treeTree file resulting from BI with a dataset that includes molecular data from De-Silva et al. 2017.mol_only_beast.treML tree (molecular data)Tree file resulting from ML analysis with a dataset that includes molecular data from De-Silva et al. 2017.mol_only_iqtree.treML tree (morphology data)Tree file resulting from ML analysis with a dataset that includes morphology data from De-Silva et al. 2017.morph_only_iqtree.tre
DOI: 10.5061/dryad.df264
title: Data from: Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

description: The origin of eukaryotes represents an enigmatic puzzle, which is still
 lacking a number of essential pieces. Whereas it is currently accepted
 that the process of eukaryogenesis involved an interplay between a host
 cell and an alphaproteobacterial endosymbiont, we currently lack detailed
 information regarding the identity and nature of these players. A number
 of studies have provided increasing support for the emergence of the
 eukaryotic host cell from within the archaeal domain of life, displaying a
 specific affiliation with the archaeal TACK superphylum. Recent studies
 have shown that genomic exploration of yet-uncultivated archaea, the
 so-called archaeal ‘dark matter’, is able to provide unprecedented
 insights into the process of eukaryogenesis. Here, we provide an overview
 of state-of-the-art cultivation-independent approaches, and demonstrate
 how these methods were used to obtain draft genome sequences of several
 novel members of the TACK superphylum, including Lokiarchaeum, two
 representatives of the Miscellaneous Crenarchaeotal Group
 (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of
 cultivation-independent genomics approaches, as well as future
 developments in next-generation sequencing technologies, will
 revolutionize our current view of microbial evolution and diversity, and
 provide profound new insights into the early evolution of life, including
 the enigmatic origin of the eukaryotic cell.
description: Supplementary
 datasuppl_data.tar.gz
DOI: 10.5061/dryad.p3fg9
title: Data from: Biocontrol insect impacts population growth of its target plant species but not an incidentally used nontarget

description: Understanding the impact of herbivory on plant populations is a
 fundamental goal of ecology. Damage to individual plants can be visually
 striking and affect the fates of individuals, but these impacts do not
 necessarily translate into population-level differences in vital rates
 (survival, growth, or fecundity) or population growth rates. In biological
 control of weeds, quantitative assessments of population-level impacts of
 released agents on both target invasive plants and native, nontarget
 plants are needed to inform evaluations of the benefits and risks of
 releasing agents into new regions. Here we present a 3-yr experimental
 demographic field study using the European root-feeding biocontrol weevil,
 Mogulones crucifer, first released in Canada in 1997 to control the
 invasive weed Cynoglossum officinale (Boraginaceae). Mogulones crucifer is
 an effective “search and destroy” agent in Canada, but sporadically feeds,
 oviposits, and develops on native nontarget Boraginaceae. We investigated
 the population-level impacts of this biocontrol insect on its target weed
 and a native nontarget plant, Hackelia micrantha (Boraginaceae), by
 releasing large numbers of weevils into naturally occurring patches of H.
 micrantha growing isolated from or interspersed with C. officinale. We
 followed the fates of individual plants on release and nonrelease
 (control) sites for two transition years, developed matrix models to
 project population growth rates (λ) for each plant species, and examined
 the contributions from differences in vital rates to changes in λ using
 life table response experiments (LTRE). In contrast to studies of the
 insect–plant interaction in its native range, as a biocontrol agent, M.
 crucifer increased mortality of C. officinale rosettes in the year
 immediately following release, depressing the weed's λ to below the
 population replacement level. However, λ for H. micrantha was never
 depressed below the replacement level, and any differences between release
 and nonrelease sites in the nontarget could not be explained by
 significant contributions from vital rates in the LTRE. This study is the
 first to simultaneously and experimentally examine target and nontarget
 population-level impacts of a weed biocontrol insect in the field, and
 supports the theoretical prediction that plant life history
 characteristics and uneven herbivore host preferences can interact to
 produce differences in population-level impacts between target and
 nontarget plant species.
description: Catton et al Demography
 Stacked April 12 2015Demography data for
 Cynoglossum officinale and Hackelia micrantha on Mogulones crucifer
 release and nonrelease sites used in the Catton et al. (2016) publication
 in Ecosphere.