cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h18931zmz
title: Behavior and diet data collected from i) GPS video camera collars and ii) fecal samples collected from individuals from the Fortymile Caribou Herd

description: Summer diets are crucial for large herbivores in the subarctic and are
 affected by weather, harassment from insects and a variety of
 environmental changes linked to climate. Yet understanding foraging
 behavior and diet of large herbivores is challenging in the subarctic
 because of their remote ranges. We used GPS video-camera collars to
 observe behaviors and summer diets of the migratory Fortymile Caribou Herd
 (Rangifer tarandus granti) across Alaska, USA and the Yukon, Canada.
 First, we characterized caribou behavior. Second, we tested if videos
 could be used to quantify changes in the probability of eating events.
 Third, we estimated summer diets at the finest taxonomic resolution
 possible through videos. Finally, we compared summer diet estimates from
 video collars to microhistological analysis of fecal pellets. We
 classified 18,134 videos from 30 female caribou over two summers (2018 –
 2019). Caribou behaviors included eating (mean = 43.5%), ruminating
 (25.6%), travelling (14.0%), stationary awake (11.3%) and napping (5.1%).
 Eating was restricted by insect harassment. We classified forage(s)
 consumed in 5,549 videos where diet composition (monthly) highlighted a
 strong tradeoff between lichens and shrubs; shrubs dominated diets in June
 and July when lichen use declined. We identified 63 species, 70 genus and
 33 family groups of summer forages from videos. After adjusting for
 digestibility, monthly estimates of diet composition were strongly
 correlated at the scale of the forage functional type (i.e., forage groups
 comprised of forbs, graminoids, mosses, shrubs, and lichens; r = 0.79, p
 &lt; 0.01). Using video collars, we identified i) a pronounced
 tradeoff in summer foraging between lichens and shrubs and ii) the costs
 of insect harassment on eating. Understanding caribou foraging ecology is
 needed to plan for their long-term conservation across the circumpolar
 north and video collars can provide a powerful approach across remote
 regions.
description: This dataset was collected from GPS video-camera collars worn by
 female caribou of the Fortymile Caribou Herd spanning Alaska, USA and
 Yukon, Canada.
description: README files attached to each .csv file in the uploaded file
 set.
DOI: 10.5061/dryad.2v6wwpzph
title: Data from: Diet composition of reintroduced Red-and-Green Macaws (Ara chloropterus) reflects gradual adaptation to life in the wild

description: Over the last two centuries, the Red-and-Green Macaw (Ara chloropterus)
 has become locally extinct in Argentina. In an attempt to restore its key
 ecosystem functions as both disperser and regulator of large-seeded
 plants, a reintroduction project was initiated at the Iberá National Park
 in northeastern Argentina. The ability of released individuals to find
 food is crucial, especially when working with captive-bred animals, as
 long-term establishment of a self-sustaining population depends on their
 short-term ability to exploit wild food sources. Monitoring of feeding
 habits is usually conducted through behavioral observation, but in recent
 years DNA metabarcoding has emerged as an alternative for obtaining highly
 resolved data on diet composition. In this study, we use a combination of
 both techniques to characterize the breadth and composition of the
 reintroduced macaws’ diet. In addition, we compare the efficiency of both
 observational and molecular techniques to assess diet composition in a
 frugivorous bird. Individuals fed on a variety of plant species (n = 49)
 belonging to a broad phylogenetic spectrum (28 families). Dietary richness
 estimated by direct observation and DNA metabarcoding was similar, though
 smaller than the combination of the two datasets as both techniques
 detected at least 15 species not recorded by the other method. While the
 total number of detected species was higher for observational data, the
 rate of species-detection per sampling day was higher for DNA
 metabarcoding. These results suggest that a combination of both methods is
 required in order to obtain the most accurate account of the total
 diversity of the diet of a bird species. The ability of reintroduced
 macaws to successfully exploit local food resources throughout the year
 indicates a good level of adjustment to the release site, an important
 step towards the creation of a stable, self-sustaining population of
 Red-and-Green Macaws in Northern Argentina.
description: <strong>Reference library.fasta:</strong> plant
 species sequences included in the reference library. The sequence names
 consist of a combination of GI numbers and species names.
 <strong>Macaw_diet_dataset.xlsx: </strong>consists
 of<strong> </strong>three spreadsheets: 
 Observational data: observed feeding events by reintroduced
 Red-and-Green Macaws Fecal samples: date and time of
 collection of fecal samples Metabarcoding results:
 taxa detected in fecal samples
DOI: 10.5061/dryad.d2547d83s
title: Supporting data from: Characterizing changes in eastern U.S. pollution events in a warming world

description: Risk assessments of air pollution impacts on human health and ecosystems
 would ideally consider a broad set of climate and emission scenarios, as
 well as natural internal climate variability. We analyze initial condition
 chemistry-climate ensembles to gauge the significance of
 greenhouse-gas-induced air pollution changes relative to internal climate
 variability, and consider response differences in two models. To quantify
 the effects of climate change on the frequency and duration of summertime
 regional-scale pollution episodes over the Eastern United States (EUS), we
 apply an Empirical Orthogonal Function (EOF) analysis to a 3-member
 GFDL-CM3 ensemble with prognostic ozone and aerosols and a 12-member
 NCAR-CESM1 ensemble with prognostic aerosols under a 21st century RCP8.5
 scenario with air pollutant emissions frozen in 2005. Correlations between
 GFDL-CM3 principal components for ozone, PM2.5 and temperature represent
 spatiotemporal relationships discerned previously from observational
 analysis. Over the Northeast region, both models simulate summertime
 surface temperature increases of over 4 C from 2006–2025 to 2081–2100 and
 PM2.5 of up to 1–4 μg m−3. The ensemble average decadal incidence of upper
 quartile Northeast PM2.5 events lasting at least three days doubles in
 GFDL-CM3 and increases by ∼50% in CESM1. In other EUS regions, inter-model
 differences in PM2.5 responses to climate change cannot be explained
 solely by internal climate variability. Our EOF-based approach anticipates
 future opportunities to data-mine initial condition chemistry-climate
 model ensembles for probabilistic assessments of changing regional-scale
 pollution and heat event frequency and duration, while obviating the need
 to bias-correct concentration-based thresholds separately in individual
 models.
description: See README.TXT
DOI: 10.25338/b8463x
title: Anesthetic pharmacology of the mint extracts L-carvone and methyl salicylate

description: Introduction: Hydrocarbons with sufficient water solubility allosterically
 modulate anesthetic-sensitive ion channels. Mint extracts L-carvone and
 methyl salicylate water solubility exceeds modulation cutoff values for
 γ-amino butyric acid type A (GABAA) receptors, N-methyl-D-aspartate (NMDA)
 receptors, and type-2 voltage-gated sodium (Nav1.2) channels. We
 hypothesized that mint extracts modulate these channels at concentrations
 that anesthetize rats. Methods:Channels were expressed separately in frog
 oocytes and studied using 2-electrode voltage clamp techniques at drug
 concentrations up to 10 mM. Normalized current effects were fit to Hill
 equations. Mint compounds were formulated in a lipid emulsion and
 administered IV to rats. When unresponsive to the tail clamp, rats were
 exsanguinated, and plasma drug concentrations were measured. Results: Both
 mint compounds caused concentration-dependent inhibition of all channels
 except for methyl salicylate which inhibited GABAA receptors at low
 concentrations and potentiated at high concentrations. Plasma drug
 concentrations in anesthetized rats were 7.9 mM for L-carvone and 2.7 mM
 for methyl salicylate. This corresponded to ≥53% NMDA receptor inhibition
 and ≥78% Nav1.2 channel inhibition by both compounds and 30% potentiation
 of GABAA receptors by methyl salicylate. Conclusion: L-Carvone and methyl
 salicylate allosterically modulate cell receptor targets important to
 molecular actions of conventional anesthetics at concentrations that also
 induce general anesthesia in rats.
description: Animal data collected in Sprague-Dawley rats.
 Electrophysiology data collected using two-electrode voltage
 clamp techniques.
description: Electrophysiology data includes actual measured data and a
 separate column with responses fit to a Hill equation.
DOI: 10.5061/dryad.m63xsj435
title: Deep-time structural evolution of retroviral and filoviral surface envelope proteins

description: The retroviral surface envelope protein subunit (SU) mediates receptor
 binding and triggers membrane fusion by the transmembrane (TM) subunit. SU
 evolves rapidly under strong selective conditions, resulting in seemingly
 unrelated SU structures in highly divergent retroviruses. Structural
 modeling of the SUs of several retroviruses and related endogenous
 retroviral elements with AlphaFold 2 identifies a TM-proximal SU
 β-sandwich structure that has been conserved in the orthoretroviruses for
 at least 110 million years. The SU of orthoretroviruses diversified by the
 differential expansion of the β-sandwich core to form domains involved in
 virus-host interactions. The β-sandwich domain is also conserved in the SU
 equivalent GP1 of Ebola virus although with a significantly
 different orientation in the trimeric envelope protein structure relative
 to the β-sandwich of human immunodeficiency virus type 1 gp120, with
 significant evidence for divergent rather than convergent evolution. The
 unified structural view of orthoretroviral SU and filoviral
 GP1 identifies an ancient, structurally conserved, and evolvable
 domain underlying the structural diversity of orthoretroviral SU and
 filoviral GP1.
description: Models for orthoretroviral SU were genenerated with AlphaFold
 2. A simplified version25 of Alphafold 2 run on the ColabFold server with
 graphical processing unit support accessible at
 https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb was used for modeling with templates, without amber relaxation and homooligomer set to 1. Comparable models were obtained by modeling with or without templates or amber relaxation.
description: pLDDT scores in B-factor column 11.
DOI: 10.5061/dryad.69p8cz937
title: Aralia elata genome and annotation

description: We report a chromosome-level genome of Aralia elata with a total length of
 1.08 Gb and a contig N50 of 1.2 Mb using SMRT, HiC, and next-generation
 sequencing. The Aralia elata genome is the first chromosome-level genome
 of genus Aralia. This dataset also includes the annotation of Aralia elata
 genome and the gene expression profiles.
description: Genomic DNA was extracted from a young leaf sample on a 5-year-old plant of <em>Aralia elata</em>, which was collected from Harbin, Heilongjiang Province, China, using the DNAsecure Plant Kit (TIANGEN) and broken into random fragments. Short-read libraries were constructed according to the manufacturer’s instructions (Illumina, San Diego, CA) and then sequenced on an Illumina HiSeq 4000 system at the Beijing Genomics Institute-Shenzhen (BGI-Shenzhen).For PacBio libraries, the whole genome was sequenced on the PacBio Sequel II System based on single-molecule real-time (SMRT) sequencing technology, and 99.88 Gb (~90.6×) of data were obtained.   We combined three strategies to predict genes in the <em>A. elata</em> genome: homology-based, de novo, and RNA-Seq data alignment. Total RNA was extracted from four tissues (root, stem, leaf, and seed, with three biological repeats) using an RNA extraction kit (Huayueyang, ZH120, China). The mRNA from all samples was purified using the TruSeq RNA Sample Prep Kit (Illumina), followed by sequencing on an Illumina HiSeq 4000 sequencer. We used MCSCAN python-version (v1.1.18) to identify the synteny between <em>A. elata</em> and other species.
description: "AE.chrom_level.genome.fa" is the chromosome-level
 genome file of Aralia elata.
 "AE.maker.final.chrom_level.gene.gff" is the
 annotations of Aralia elata's genome,including gene, mRNA, cds, exon
 and UTR. "AE.genes.fpkm.txt" is the gene
 expression profile of different tissues of Aralia elata which used FPKM
 value. "R_AE_Le2","R_AE_Le4","R_AE_Le6"
 indicate the leaf of Aralia elata with three repeats.
 "R_AE_St2","R_AE_St4","R_AE_St6" indicate
 the stem of Aralia elata with three repeats.
 "R_AE_Ro","R-AE-RoA-2","R-AE-RoA" indicate
 the root of Aralia elata with three replicates.
 "R_AE_Se","R-AE-SeA","R-AE-SeA-2" indicate
 the seed of Aralia elata with three replicates.
 "ae.ae.lifted.anchors" is the paralogous groups in
 Aralia elata by using python version MACSCAN(JCVI).
 "AE.maker.final.chrom_level.gene.cds.fa" is the cds
 sequences of Aralia elata.
 "AE.maker.final.chrom_level.gene.pep.fa" is the protein
 sequences of Aralia elata.
DOI: 10.5061/dryad.vq83bk3tc
title: Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

description: Northern Hemisphere forests changed drastically in the early Eocene with
 the diversification of the oak family (Fagaceae). Cooling climates over
 the next 20 million years fostered the spread of temperate biomes that
 became increasingly dominated by oaks and their chestnut relatives. Here
 we investigate the timing and pattern of major macroevolutionary events
 and ancient genome-wide signatures of hybridization across Fagaceae. An
 unparalleled transformation of forest dynamics began with the rapid
 diversification of major lineages within 15 million years following the
 K-Pg extinction. Innovations related to seed and pollen dispersal are
 implicated in triggering waves of continental radiations, while fungal
 symbioses fortified a competitive edge underground. We detected
 introgression at multiple time scales, including ancient events predating
 the origination of genus-level diversity. As oak lineages moved into newly
 available temperate habitats in the early Miocene, secondary contact
 between previously isolated species occurred. This resulted in adaptive
 introgression, further amplifying global proliferation.
description: To generate the nuclear DNA sequences, we sequenced whole genomes
 of 117 individuals to a coverage of 25-40× using the Illumina NovaSeq
 platform and called genotypes in SCGs regions. We trimmed and filtered raw
 reads using trimmomatic v0.39, mapped high quality reads to a reference
 genome using BWA, and called genotypes via HaplotypeCaller in GATK v4.2.
 We called all available sites (both variants and invariants).
 For plasomes, raw reads from whole genome sequencing were used
 for <i>de novo</i> assembly of plastomes in NOVOPlasty v4.2.
 Assembled plastomes were annotated using the program PGA. The boundaries
 of inverted repeats and coding regions of each annotated gene were
 determined in Geneious 7.1.4 by using the <i>Q. rubra</i>
 plastome as a reference. Coding regions of 76 protein-coding genes present
 in all species were extracted from the assemblies, aligned using MAFFT
 7.221, and manually adjusted using Bioedit v.7.2
 (https://bioedit.software.informer.com).
DOI: 10.5061/dryad.pg4f4qrqp
title: Nucleotide sequences in Procambarus clarkii

description: Crayfish is a model for studying the effect of light on locomotor activity
 and neuroendocrine functions. In this study, we have described 62
 transcripts from the pleonal nerve cord of the crayfish, using
 bioinformatics tools that identify phylogenetic families of genes related
 to the light interaction in the extraretinal photoreceptors. We deposited
 all sequencing data in the GenBank database. Here
 shows supplemental data from the freshwater crayfish Procambarus
 clarkii. The results suggest that the genes related to ocular and
 extraocular light perception in the crayfish P. clarkii
 use common biosynthesis pathways and phototransduction cascades.
description: Total RNA was extracted from the abdominal nerve cord using
 TRIzol reagent following the manufacturer’s protocol (Catalog number
 15596018, Invitrogen Co., Carlsbad, CA, USA).  We used 5μg of total RNA to
 obtain the cDNA libraries, according to the manufacturer’s protocol for
 the Illumina TruSeq RNA Library Preparation Kit v2 (Catalog number
 RS-122-2001, Illumina, San Diego, CA, USA). We performed Illumina
 paired-end protocol 150 bp sequencing. The library obtained was sequenced
 using the MiSeq Reagent kit v3 system (Catalog number MS-102-3001)
 according to the manufacturer’s protocol, to obtain the peonal nerve cord
 transcriptome.  Methods for processing the data:
 Bioinformatic analysis. 
description: Please see Readme file:
 "Calderón-_Rosete_et_al.__2021._Dataset_Readme.txt"
DOI: 10.15468/dl.etacgq
title: Occurrence Download

description: A dataset containing 1591 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((29.47779 -29.85751,29.52608 -29.85701,29.5244 -29.79565,29.47679 -29.79665,29.47779 -29.85751))",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 1591 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002975-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gxd2547nj
title: Patch size drives colonization by aquatic insects, with minor priority effects of a cohabitant

description: Patch size is one of the most important factors affecting the distribution
 and abundance of species, and recent research has shown that patch size is
 an important niche dimension affecting community structure in aquatic
 insects. Building on this result, we examined the impact of patch size in
 conjunction with presence of larval anurans on colonization by aquatic
 insects. Hyla chrysoscelis (Cope’s gray treefrog) larvae are abundant and
 early colonists in fishless lentic habitats, and these larvae can fill
 multiple ecological roles. By establishing larvae in mesocosms prior to
 colonization, we were able to assess if H. chrysoscelis larvae have
 priority effects on aquatic insect assemblages. We conducted a series of
 three experiments in naturally-colonized experimental landscapes to test
 whether (1) H. chrysoscelis larval density affects insect colonization,
 (2) variation in patch size affects insect colonization, and (3) the
 presence and larval density of H. chrysoscelis shifts colonization of
 insects between patches of different size. Larval density independently
 had almost no effect on colonization, while patch size had
 species-specific effects consistent with prior work. When larvae and patch
 size were tested in conjunction, patch size had numerous, often strong,
 species-specific effects on colonization; larval density had effects
 largely limited to the assemblages of colonizing beetles and water bugs,
 with few effects on individual species. Higher larval densities in large
 mesocosms shifted some insect colonization to smaller patches, resulting
 in higher beta diversity among small patches in proximity to high density
 large mesocosms. This indicates establishing H. chrysoscelis larvae prior
 to insect colonization can likely create priority effects that slightly
 shape insect communities. Our results support the importance of patch size
 in studying species abundances and distributions, and also indicate that
 colonization order plays an important role in determining the communities
 found within habitat patches.
description: See Methods of paper.
description: See ReadMe file.
DOI: 10.5061/dryad.3bk3j9kkw
title: Divided by the range: evidence for geographic isolation of the highly mobile Emu (Dromaius novaehollandiae)

description: Conserving evolutionary processes is becoming increasingly important in
 conservation management as environmental changes threaten wild
 populations. Characterising genetically distinct populations and assessing
 connectivity across the landscape enables wildlife managers to prioritise
 conservation efforts with limited resources. In the NSW North Coast
 bioregion of Australia, one of the last remaining coastal populations of
 the Emu (Dromaius novaehollandiae) has been state-listed as an Endangered
 Population, owing to its geographic isolation and small census size. Using
 mitochondrial and nuclear genetic markers, we examined the spatial genetic
 structure of Emus across south-eastern Australia and assessed the
 effective population size (Ne) and genetic diversity of the NSW North
 Coast Emu to inform management. We show significant genetic divergence
 between the NSW North Coast Emu and other localities based on thousands of
 highly resolving nuclear markers, which was not explained by geographic
 distance. Among NSW North Coast Emus, we found less genetic diversity and
 a critically low effective population size (Ne = 14.84 and 22.49
 based on independent methods). Together, these findings suggest that the
 NSW North Coast Emu is at risk of further losses of genetic diversity and
 inbreeding depression. Incorporating genetic data into the design of
 captive-release and translocation projects would refine management plans
 for this locally important population and monitor risks to its long-term
 survival.
description: The data were collected as part of a population genetics study
 investigating gene flow and effective population sizes of Emus (Dromaius
 novaehollandiae) across south-east Australia. Feather and tissue samples
 were collected non-invasively and extracted DNA was sequenced via
 genotyping-by-sequencing methods employed by Diversity Arrays Technology,
 Canberra, Australia. Resulting single nucleotide polymorphisms (SNPs) were
 filtered for quality (see ReadMe file).
description: See the ReadMe file for details on file formats and filtering
 procedures
DOI: 10.5061/dryad.g4f4qrfrg
title: Data set: Reproductive character displacement in genital morphology in Ohomopterus ground beetles

description: Genital morphology reveals rapid diversification among species, and
 species-specific divergence in genital morphology may result in
 reproductive isolation and promote speciation. Natural selection against
 maladaptive hybridization may cause species-specific genital divergence.
 In this context, divergence in mating traits is expected to be greater
 between sympatric populations than between allopatric populations in a
 pair of species, known as reproductive character displacement (RCD).
 However, there are few examples of RCD in the genital morphology of
 closely related species. Additionally, processes leading to RCD have
 rarely been inferred. In this study, we examined RCD and its underlying
 mechanisms by focusing on species-specific genital morphologies of closely
 related Ohomopterusground beetle species. A morphological
 analysis showed patterns of RCD in species-specific genital parts in both
 sexes. Interspecific hybridization was confirmed by a mate choice
 experiment and by a population genetic analysis indicating extensive
 interspecific gene flow, suggesting that reinforcement is the most
 plausible process underlying the observed RCD. We found variation in the
 degree of displacement in contact zones, which may correspond with the
 ongoing process of genital evolution and speciation. Our results provide
 support for the lock-and-key hypothesis of genital evolution in closely
 related Ohomopterus species.