cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kkwh70s5v
title: Deriving population scaling rules from individual-level metabolism and life history traits - Code and Data

description: Individual metabolism generally scales with body mass with an exponent
 around 3/4. From dimensional arguments it follows that maximum population
 growth rate (rmax) scales with a -1/4 exponent. However, the
 dimensional argument implicitly assumes that offspring size is
 proportional to adult size. Here we calculate rmax from metabolic scaling
 at the level of individuals within size-structured populations while
 explicitly accounting for offspring size. We identify four general
 patterns of how rmax scales with adult mass based on four empirical
 life-history patterns employed by groups of species. These life-history
 patterns are determined by how traits of somatic growth rate and/or
 offspring mass relate to adult mass. One life-history pattern -- constant
 adult:offspring mass ratio and somatic growth rate independent of adult
 mass -- leads to the classic -1/4 scaling of rmax. The
 other three life-history patterns lead either to non-metabolic population
 growth scaling with adult mass or do not follow a power-law relationship
 at all. Using life-history data of five marine taxa and terrestrial
 mammals, we identify species groups that belong to one of each case. We
 predict that elasmobranchs, copepods, and mammals follow standard
 -1/4 power-law scaling, whereas teleost fish and bivalves do not
 have a pure power-law scaling. Our work highlights how taxa may deviate
 from the classic -1/4 metabolic scaling pattern of maximum
 population growth. The approach is generic and can be applied to any taxa.
description: Description of the scripts and data<br> (Data are in both
 ".mat" and ".csv") 
 Base_run function: contains all the scripts for the figures in
 Denéchère et al 2021. Parameters function: Data are
 loaded and processed from the parameter function that contains information
 about each data file: value, units, and definition of all the
 parameters.  Pop_growth_rate:  Contains the Rmax
 equation and associated parameters for each taxon.
 Grid function: used to create a log scale
 Ciplot function is used to create shadow areas. Created by:
 Raymond Reynolds 24/11/06; updated by Pham Thai Binh
 12/06/2017.
DOI: 10.5061/dryad.g1jwstqs1
title: Population-specific responses of an insect herbivore to variation in host-plant quality

description: Anthropogenic climate change poses a substantial challenge to many
 organisms, to which they need to respond to avoid fitness reductions.
 Investigating responses to environmental change is particularly
 interesting in herbivores, as they are potentially affected by indirect
 effects mediated via variation in host-plant quality. We here use the
 herbivorous insect Pieris napi to investigate geographic variation in the
 response to variation in food quality. We performed a common garden
 experiment using replicated populations from Germany and Italy, and
 manipulating host quality by growing host plants at different temperature
 and water regimes. We found that feeding on plants grown at a higher
 temperature generally diminished the performance of P. napi, evidenced by
 a prolonged development time and reduced larval growth rate, body mass,
 fat content, and phenoloxidase activity. Genotype by environment
 interactions (G x E) were present in several performance traits,
 indicating that Italian populations (1) respond more strongly to variation
 in host-plant quality and (2) are more sensitive to poor food quality than
 German ones. This may reflect a cost of the rapid lifestyle found in
 Italian populations. Consequently, German populations may be more
 resilient against environmental perturbations and may perhaps even benefit
 from warmer temperatures, while Italian populations will likely suffer
 from the concomitantly reduced host-plant quality. Our study thus
 exemplifies how investigating G x E may help to better understand the
 vulnerability of populations to climate change.
DOI: 10.5061/dryad.pc866t1q7
title: Data from: Sequential use of niche and occupancy models identifies conservation and research priority areas for two data-poor endemic birds from the Colombian Andes

description: The lack of high-quality information on data-poor species can hinder
 efforts to inform conservation actions via spatial distribution modeling.
 This is particularly true for tropical birds of conservation concern, for
 which ecological studies and assessments of their conservation status have
 received limited funding. Here we use a cost- and time-efficient protocol
 for assessing the distribution of range-restricted taxa and to identify
 priority areas for their conservation based on a sequential application of
 Environmental Niche Models (ENMs) and Occupancy-Detection Models. This
 approach first uses available geographical information and niche-theory to
 prioritize potential study sites, which can later be surveyed to obtain
 high-quality presence-absence data to accurately model distributional
 ranges with limited resources. We apply this protocol to identify priority
 areas for two Neotropical birds of conservation concern endemic to the
 Colombian Andes: Yellow-headed Brush-finch (Atlapetes flaviceps) and
 Tolima Dove (Leptotila conoveri). We first fitted ENMs using
 spatially-filtered datasets containing all available records up to 2018.
 We then conducted field surveys across climatically suitable areas
 identified for both species, carrying out a total of 1750 counts to
 generate input data for the occupancy models. Overall, our results
 suggested more extended and more continuous distribution ranges for both
 species than previously reported, but also identified population
 strongholds that are not currently represented within the national
 protected areas system. Both species occupied a narrow elevational belt
 (~1300–2600) of the Central Andes of Colombia primarily on the slopes of
 the Magdalena River valley, with isolated populations in the Western and
 Eastern Andes; these areas have undergone some of the most marked
 landscape transformations in Colombia. This straightforward protocol
 maximizes available information and minimizes costs, while allowing for
 estimation of occurrence probabilities for range-restricted, data-poor
 taxa.
description: A detailed description on usage can be found in the ReadMe.txt
 file.
DOI: 10.5061/dryad.qnk98sfj1
title: Data for: A neural circuit for wind-guided olfactory navigation

description: To navigate towards a food source, animals must frequently combine odor
 cues that tell them what sources are useful with wind direction cues that
 tell them where the source can be found.  Where and how
 these two cues are integrated to support navigation is
 unclear.  Here we identify a pathway to
 the Drosophila fan-shaped body (FB) that encodes
 attractive odor and promotes upwind navigation. We show that neurons
 throughout this pathway encode odor, but not wind direction. Using
 connectomics, we identify FB local neurons called h∆C that receive input
 from this odor pathway and a previously described wind
 pathway.  We show that h∆C neurons exhibit odor-gated,
 wind direction-tuned activity, that sparse activation of h∆C neurons
 promotes navigation in a reproducible direction, and that h∆C activity is
 required for persistent upwind orientation during
 odor.  Based on connectome data, we develop a
 computational model showing how h∆C activity can promote navigation
 towards a goal such as an upwind odor source.  Our
 results suggest that odor and wind cues are processed by separate pathways
 and integrated within the FB to support goal-directed navigation.
description: Behavioral data collected using a high-throughput wind tunnel
 paradigm in response to odor and optogenetic activation of different
 neural groups. 2-photon calcium imaging data in
 response to odor and widn stimuli delivered from different
 directions confocal imaging data of expression patterns
 in different lines Computational modeling
 data
description: Please see attached readme files and publication.
DOI: 10.15468/dl.frx5ja
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Happywhale - Polar bear in Arctic Ocean"
 ]
}

 The dataset includes 66 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002990-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n02v6wwzr
title: E-scape: consumer-specific landscapes of energetic resources derived from stable isotope analysis and remote sensing

description: Energetic resources and habitat distribution are inherently linked.
 Energetic resource availability is a major driver of the distribution of
 consumers, but estimating how much specific habitats contribute to the
 energetic resource needs of a consumer can be problematic. We present a
 new approach that combines remote sensing information and stable isotope
 ecology to produce maps of energetic resources (E-scapes). E-scapes
 project species-specific resource use information onto the landscape to
 classify areas based on energetic importance. Using our E-scapes, we
 investigated the relationship between energetic resource distribution and
 white shrimp distribution and how the scale used to generate the E-scape
 mediated this relationship. E-scapes successfully predicted the size,
 abundance, biomass, and total energy of a consumer in salt marsh habitats
 in coastal Louisiana, USA at scales relevant to the movement of the
 consumer. Our E-scape maps can be used alone or in combination with
 existing models to improve habitat management and restoration practices
 and have potential to be used to test fundamental movement
 theory. 
description: White shrimp were collected in Port Fourchon, LA and frozen until
 processed in the lab. Biomass and abundance of shrimp at each location was
 calculated by measuring all shrimp collected in a drop sampler (1
 m<sup>2</sup>) at each location. Five shrimp were pooled at
 each sampling location and run for stable isotope analysis of carbon,
 nitrogen, and sulfur and bomb calorimetry.
DOI: 10.5061/dryad.280gb5mr4
title: Data from: Effects of arousal and movement on secondary somatosensory and visual thalamus

description: Neocortical sensory areas have associated primary and secondary thalamic
 nuclei. While primary nuclei transmit sensory information to cortex,
 secondary nuclei remain poorly understood. We recorded juxtasomally from
 secondary somatosensory (POm) and visual (LP) nuclei of awake mice while
 tracking whisking and pupil size. POm activity correlated with whisking,
 but not precise whisker kinematics. This coarse movement modulation
 persisted after facial paralysis and thus was not due to sensory
 reafference. This phenomenon also continued during optogenetic silencing
 of somatosensory and motor cortex and after lesion of superior colliculus,
 ruling out a motor efference copy mechanism. Whisking and pupil dilation
 were strongly correlated, possibly reflecting arousal. Indeed LP, which is
 not part of the whisker system, tracked whisking equally well, further
 indicating that POm activity does not encode whisker movement per se. The
 semblance of movement-related activity is likely instead a global effect
 of arousal on both nuclei. We conclude that secondary thalamus monitors
 behavioral state, rather than movement, and may exist to alter cortical
 activity accordingly.
description: Data were acquired using custom-written LabView software or
 OpenEphys. Data have been preprocessed in Matlab.
description: The readme file documents the organization of data in .mat files
 and how to relate this to the analyses in the manuscript. It also explains
 the meaning of each column.
DOI: 10.6071/m3st0g
title: Yangtze River basin ecological and hydrogeomorphic data relevant to regional hydrologic classification for sustainable dam operation

description: While some rivers have been modified and regulated for centuries
 requiring recovery efforts and restoration, other rivers are
 currently under development and facing the challenges of environmental
 degradation and loss of ecological functionality. As countries,
 such as China, expand current infrastructure to develop and
 construct flood reduction, hydropower, and water storage facilities along
 their rivers, the threat of detrimental ecological impacts expands too. To
 address these pressing challenges, this data set was used in the
 referenced article's analysis. Climatic, hydrogeomorphic, ecological,
 and anthropogenic characteristics summarized in this dataset were analyzed
 to determine the key principal components relevant to decision-making for
 environmental flows in the river basin. This resulting dataset
 includes a summary of the applied variables by subbasin cluster as
 discussed in detail in the article.
description: Data was collected from global data sets compiled within
 HydroATLAS and MODIS supported datasets in other publications. Variables
 with monthly information were aggregated to quarterly for
 analysis. Variables were evaluated for their relevent
 influence to e-flows with a pricipal component analysis (PCA) applied to
 the dataset. With the results from the PCA, the list of variables was
 reduced to the most important or pricipal components. K-means clustering
 facilitated the grouping of subbasins according to the characteristics and
 variable values.  This table includes those values used
 in clustering.
description: This data set includes annual, quarterly, monthly, and/or
 coefficient of variance means, medians, minimum values, and maximum values
 which were derived from monthly data within the original data set as cited
 in (Linke et al. 2019; Friedl and Sulla-Menashe 2019). Refer to the
 original HydroATLAS data (Linke et al. 2019) and other information found
 in the article's references for the full list of available variables
 and the complete dataset for all months and variables.
DOI: 10.5061/dryad.wdbrv15qb
title: Data from: Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation–dependent and –independent mechanisms

description: The mouse Igf2/H19 locus is regulated by genomic imprinting, in which the
 paternally methylated H19 imprinting control region (ICR) plays a critical
 role in mono-allelic expression of the genes in the locus. Although the
 maternal allele–specific insulator activity of the H19 ICR in regulating
 imprinted Igf2 expression has been well established, the detailed
 mechanism by which the H19 ICR controls mono-allelic H19 gene expression
 has not been fully elucidated. In this study, we evaluated the effect of
 H19 ICR orientation on imprinting regulation in mutant mice in which the
 H19 ICR sequence was inverted at the endogenous locus. When the
 inverted-ICR allele was paternally inherited, the methylation level of the
 H19 promoter was decreased and the H19 gene was derepressed, suggesting
 that methylation of the H19 promoter is essential for complete repression
 of H19 gene expression. Unexpectedly, when the inverted allele was
 maternally inherited, the expression level of the H19 gene was lower than
 that of the WT allele, even though the H19 promoter remained fully
 hypomethylated. These observations suggested that the polarity of the H19
 ICR is involved in controlling imprinted H19 gene expression on each
 parental allele, dependent or independent on DNA methylation of the H19
 promoter.
description: Sanger seq for Figure 2 Sanger seq for Figure
 4 Sanger seq for Supplementary Figure 3
 Sanger seq for Supplementary Figure 5 Sanger
 seq for Supplementary Figure 6 Sanger seq for
 Supplementary Figure 7 Sanger seq for Supplementary
 Figure 9 Sanger seq for Supplementary Figure
 10 Sanger seq for Supplementary Figure 11
DOI: 10.5061/dryad.0p2ngf22v
title: Trends in weather conditions favor generalist over specialist species in rear-edge alpine bird communities

description: Using the community of six passerine species breeding in the alpine zone
 of the Cantabrian mountains (NW Iberian Peninsula), we sought to document
 the changes in bird abundance across the elevational gradient during the
 last decade, evaluate the relationship between bird abundance and local
 climatic conditions (i.e. weather conditions), and discuss the mechanisms
 by which these conditions might be mediating the observed abundance trends
 in a global warming context. We estimated bird abundance at the home range
 level using point count transects and distance sampling during the
 breeding season, and fitted generalized linear mixed models to describe
 their temporal trends across the elevational gradient. We used a
 structural equation modeling approach to estimate the direct, indirect and
 total effects of weather and temporal variables, while considering the
 correlations and causal relationships among them and with the elevational
 gradient.
DOI: 10.5061/dryad.jsxksn0b7
title: Sequence-dependent model of genes with dual σ factor preference

description: Escherichia coli uses s factors to quickly control large gene cohorts
 during stress conditions. While most of its genes respond to a single s
 factor, approximately 5% of them have dual s factor preference. The most
 common are those responsive to both s70, which controls housekeeping
 genes, and s38, which activates genes during stationary growth and
 stresses. Using RNA-seq and flow-cytometry measurements, we show that
 ‘σ70+38 genes’ are nearly as upregulated in stationary growth as ‘σ38
 genes’. Moreover, we find a clear quantitative relationship between their
 promoter sequence and their response strength to changes in σ38 levels. We
 then propose and validate a sequence dependent model of σ70+38 genes, with
 dual sensitivity to s38 and s70, that is applicable in the exponential and
 stationary growth phases, as well in the transient period in between. We
 further propose a general model, applicable to other stresses and σ factor
 combinations. Given this, promoters controlling σ70+38 genes (and
 variants) could become important building blocks of synthetic circuits
 with predictable, sequence-dependent sensitivity to transitions between
 the exponential and stationary growth phases.
DOI: 10.5061/dryad.0rxwdbs1x
title: Data from: Evolution of flexible biting in hyperdiverse parasitoid wasps

description: One key event in insect evolution was the development of mandibles with
 two joints, which allowed powerful biting, but restricted their movement
 to a single degree of freedom. These mandibles define the Dicondylia,
 which constitute over 99 percent of all extant insect species. It was
 common doctrine that the dicondylic articulation of chewing mandibles
 remained unaltered for more than 400 million years. We report highly
 modified mandibles overcoming the restrictions of a single degree of
 freedom and hypothesize their major role in insect diversification. These
 mandibles are defining features of parasitoid chalcid wasps, one of the
 most species-rich lineages of insects. The shift from powerful chewing to
 precise cutting likely facilitated adaptations to parasitize hosts hidden
 in hard substrates, which pose challenges to the emerging wasps. We reveal
 a crucial step in insect evolution and highlight the importance of
 comprehensive studies even of putatively well-known systems.
description: Tomographic scans of ethanol-preserved insect heads were
 performed at the UFO-I station of the Imaging Cluster at the KIT light
 source using a parallel polychromatic X-ray beam produced by a 1.5 T
 bending magnet. The beam was spectrally filtered by 0.5 mm aluminum and
 the resulting spectrum had a peak at about 15 keV, with a full-width at
 half maximum bandwidth of about 10 keV. A fast indirect detector system
 was employed, consisting of a 12 µm LSO:Tb scintillator and a diffraction
 limited optical microscope (Optique Peter) coupled with a 12bit pco.dimax
 high speed camera with 2016 x 2016 pixels. Scans were done by taking 3,000
 projections at 70 fps and an optical magnification of 10x, resulting in an
 effective pixel size of 1.22 µm. We used the control system concert for
 automated data acquisition and online reconstruction of tomographic slices
 for data quality assurance. Online and final data processing included flat
 field correction and phase retrieval of the projections based on the
 transport of intensity equation. X-ray beam parameters for algorithms in
 the data processing pipeline were computed by syris and the execution of
 the pipelines, including tomographic reconstruction, was performed by the
 UFO framework.
DOI: 10.5061/dryad.qnk98sfj2
title: Data for: Arthropod communities on young vegetated roofs are more similar to each other than to communities at ground level

description: This dataset comprises of arthropods collected with a D-vac
 vacuum sampling device from vegetated roofs and ground level habitats with
 low-growing open vegetation. Sampling was conducted during three
 consecutive years (2013, 2014 and 2015) at seven sampling sites
 distributed in the capital area of Finland. Each site included one
 vegetated roof and two closest ground level open habitats for the
 roof. Samples were collected twice in a growing season, in June
 and in August/September. Arthropods were identified using DNA
 metabarcoding technique. The
 mitochondrial cytochrome c oxidase subunit
 I gene (COI) was used as a marker in molecular identification in
 metabarcoding of arthropod samples and amplified with two
 non-overlapping complementary primer pairs (Leray and ANML). The
 dual tag indexed library were sequenced at the Helsinki
 Functional Genomics Unit (FuGU) in one Illumina MiSeq v3 300bp run.
DOI: 10.5061/dryad.8cz8w9grb
title: Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation

description: Photoreception is a ubiquitous sensory ability found across the Metazoa,
 and photoreceptive organs are intricate and diverse in their structure.
 Although the morphology of the compound eye in Drosophila and the
 single-chambered eye in vertebrates have elaborated independently, the
 amount of conservation within the 'eye' gene regulatory network
 remains controversial, with few taxa studied. To better understand the
 evolution of photoreceptive organs, we established the cephalopod
 Doryteuthis pealeii as a lophotrochozoan model for eye development.
 Utilizing histological, transcriptomic and molecular assays, we
 characterize eye formation in Doryteuthis pealeii Through lineage tracing
 and gene expression analyses, we demonstrate that cells expressing Pax and
 Six genes incorporate into the lens, cornea and iris, and the eye placode
 is the sole source of retinal tissue. Functional assays demonstrate that
 Notch signaling is required for photoreceptor cell differentiation and
 retinal organization. This comparative approach places the canon of eye
 research in traditional models into perspective, highlighting complexity
 as a result of both conserved and convergent mechanisms.
description: Squid were acquired at the Marine Biological Laboratory, Woods
 Hole, MA. Embryos were cultured at 20°C. Two embryos from the same egg sac
 of each stage, from 16-27, were prepared in TRIzol, phase separated and
 transferred to a Qiagen RNeasy column. Libraries were prepared after Meyer
 et al. (2009, 2012). Libraries were combined at equal volume and sequenced
 using 454 technology at the University of Texas, Austin. The 454 raw reads
 were processed using custom Perl scripts (https://github.com/Eli-Meyer/sequence_processing). Trimmed reads were assembled using Newbler v.2.6. Annotation was performed using BLASTX and custom Perl scripts mapped against the UniProt database. Illumina data were processed for quality using custom Perl scripts (https://github.com/Eli-Meyer/sequence_processing). All raw reads and annotated data have been deposited at the NCBI (SRA accession numbers SRP065414 and SRP066528).