cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sv67kd4
title: Data from: Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies

description: The relationship between animals and their gut flora is simultaneously one
 of the most common and most complex symbioses on Earth. Despite its
 ubiquity, our understanding of this invisible but often critical
 relationship is still in its infancy. We employed adult Neotropical
 butterflies as a study system to ask three questions: First, how does gut
 microbial community composition vary across host individuals, species and
 dietary guilds? Second, how do gut microbiota compare to food microbial
 communities? Finally, are gut flora functionally adapted to the chemical
 makeup of host foods? To answer these questions we captured nearly 300
 Costa Rican butterflies representing over 50 species, six families and two
 feeding guilds: frugivores and nectivores. We characterized bacteria and
 fungi in guts, wild fruits and wild nectars via amplicon sequencing and
 assessed the catabolic abilities of the gut microbiota via culture-based
 assays. Gut communities were distinct from food communities, suggesting
 that the gut environment acts as a filter on potential colonists.
 Nevertheless, gut flora varied widely among individuals and species. On
 average, a pair of butterflies shared 21% of their bacterial species and
 6% of their fungi. Host species explained 25-30% of variation in microbial
 communities while host diet explained 4%, suggesting that non-dietary
 aspects of host biology play a large role in structuring the butterfly gut
 flora. Much of the variation between species correlated with host
 phylogeny. Host diet was related to gut microbial function: compared to
 frugivores, nectivores’ gut flora exhibited increased catabolism of sugars
 and sugar alcohols and decreased catabolism of amino acids, carboxylic
 acids and dicarboxylic acids. Since fermented juice contains more amino
 acids and less sugar than nectar, it appears that host diet filters the
 gut flora by favoring microbes that digest compounds abundant in foods. By
 quantifying the degree to which gut communities vary among host
 individuals, species and dietary guilds and evaluating how gut microbial
 composition and catabolic potential are related to host diet, this study
 highlights the linkages between structure and function in one of the most
 complex and ubiquitous symbioses in the animal kingdom.
description: Butterfly microbiome and
 community metabolic profiling data (open format)Butterfly metadata,
 microbiome data (16s and ITS OTU tables; microbial taxonomic
 identifications; and representative fasta sequences for the OTUs) and gut
 community metabolic profiling (Biolog assay) data in .csv and .txt
 formats. See README file for additional information about individual
 files.Open_format_data.zipR script and R-formatted dataThis directory includes an R script that generates the figures from the associated manuscript, as well as butterfly metadata, microbiome (16s and ITS) data, and community metabolic profiling data in the .Rdata format. See the README for more information about individual files.R_files.zip
DOI: 10.5281/zenodo.18309180
title: Concentrations and isotopocule ratios of N2O and related parameters obtained during the incubation of Nitrosococuss oceani strain NS58

description: Spreadsheets that include data presented in the following paper submitted to JGR Biogoesciences:

Sakae Toyoda, Takeru Sato, Tatsuro Hirane, Tomoya Matsui, Taketomo Fujiwara, and Naohiro Yoshida, Acidification Stimulates N2O Production By Oceanic Nitrifying Bacteria
DOI: 10.5281/zenodo.18309181
title: Concentrations and isotopocule ratios of N2O and related parameters obtained during the incubation of Nitrosococuss oceani strain NS58

description: Spreadsheets that include data presented in the following paper submitted to JGR Biogoesciences:

Sakae Toyoda, Takeru Sato, Tatsuro Hirane, Tomoya Matsui, Taketomo Fujiwara, and Naohiro Yoshida, Acidification Stimulates N2O Production By Oceanic Nitrifying Bacteria
DOI: 10.5061/dryad.s0n4n05
title: Data from: Quantification of avian hazards to military aircraft and implications for wildlife management

description: Collisions between birds and military aircraft are common and can have
 catastrophic effects. Knowledge of relative wildlife hazards to aircraft
 (the likelihood of aircraft damage when a species is struck) is needed
 before estimating wildlife strike risk (combined frequency and severity
 component) at military airfields. Despite annual reviews of wildlife
 strike trends with civil aviation since the 1990s, little is known about
 wildlife strike trends for military aircraft. We hypothesized that species
 relative hazard scores would correlate positively with aircraft type and
 avian body mass. Only strike records identified to species that occurred
 within the U.S. (n = 36,979) and involved United States Navy or United
 States Air Force aircraft were used to calculate relative hazard scores.
 The most hazardous species to military aircraft was the snow goose (Anser
 caerulescens), followed by the common loon (Gavia immer), and a tie
 between Canada goose (Branta canadensis) and black vulture (Coragyps
 atratus). We found an association between avian body mass and relative
 hazard score (r2 = 0.76) for all military airframes. In general, relative
 hazard scores per species were higher for military than civil airframes.
 An important consideration is that hazard scores can vary depending on
 aircraft type. We found that avian body mass affected the probability of
 damage differentially per airframe. In the development of an airfield
 wildlife management plan, and absent estimates of species strike risk,
 airport wildlife biologists should prioritize management of species with
 high relative hazard scores.
description: Data for Military
 Relative Hazard ScoresAvian strike data from
 the U.S. Air Force and U.S. Navy wildlife strike databases. These data are
 filtered to only include strikes that occurred in the USA and involved
 species that were struck more than 20 times. Event.Class is the severity
 of the strike as classified by the military. Branch relates to reporting
 military branch (USAF or USN). airframe.1 details the general type of
 airframe involved in the strike. cNames is the consolidated species names
 across the datasets.RHS.data.xlsx
DOI: 10.5061/dryad.47t0b41
title: Data from: Metrics matter: the effect of parasite richness, intensity and prevalence on the evolution of host migration

description: Parasites have long been thought to influence the evolution of migration,
 but precisely determining the conditions under which this occurs by
 quantifying costs of infection remains a challenge. Here we developed a
 model that demonstrates how the metric used to describe infection
 (richness/diversity, prevalence, or intensity) shapes the prediction of
 whether migration will evolve. The model shows that predictions based on
 minimizing richness yield opposite results compared to those based on
 minimizing prevalence, with migration only selected for when minimizing
 prevalence. Consistent with these findings, empirical studies that measure
 parasite diversity typically find that migrants are worse off than
 residents, while those measuring prevalence or intensity find the
 opposite. Our own empirical analysis of fish parasite data finds that
 migrants (of all types) have higher parasite richness than residents, but
 with no significant difference in either prevalence or intensity.
description: READMEContains readme and
 notes for all files.code_databaseContains Python and R code for compiling the empirical data, plus the full empirical database.code_analysisContains R code, txt and CSV files for analyzing the empirical data.code_theoreticalContains Matlab code (.m files) and data (.mat files) for running model simulation data used for Figures 2 and 3 in the paper.fullmodelequationsContains pdf supplement for the paper with the full model equations and parameter table.
DOI: 10.5061/dryad.6p5kd34
title: Data from: Assault from all sides: hybridization and introgression threaten the already critically endangered Myuchelys georgesi (Chelonia: Chelidae)

description: Hybridization and introgression between species is remarkably common, even
 between distantly-related taxa. This suggests that the frequency of
 hybridization between species has been greatly constrained, not by
 evolutionary divergence in isolation, but by lack of opportunity. This
 constraint is being relaxed by human-mediated dispersal. Here we document
 a case where such dispersal of a widespread species of freshwater turtle
 (Emydura macquarii) into the highly restricted range of a critically
 endangered endemic turtle (Myuchelys georgesi) has provided opportunity
 for the two to hybridize. This has raised concerns about the potential
 impact of hybridization on the endemic species, and its continued
 persistence in the face of challenges brought about by habitat alteration,
 increased competition, disease, and genetic pollution. This study serves
 to highlight the risks associated with human-mediated dispersal, which can
 bring into contact species that would otherwise have never or rarely met,
 and so provide opportunity for hybridization and introgression between
 even distantly-related species with uncertain consequences for already
 threatened species.
description: DFwt18-3294.Rdata SNP
 data file in adegenet compressed format.DFwt18-3294.Rdata is a
 genlight object (adegenet] that contains the SNP data and associated
 metadata. It can be accessed and interrogated by loading it in
 R.DFwt18-3294.RdataDFwt18-3294_read.rA script to read in the data to a binary genlight object (Jombart 2008, Jombart & Ahmed 2011) to facilitate analysis. Draws on R package dartR (Gruber et al. 2018). Shows the code to create DFwt18-23294.Rdata.DFwt18-3294_analysisA script to replicate the analysis. Also draws on R package dartR (Gruber et al. 2018)Table_S1Details of individuals assigned to likelihood classes (parental Emydura macquarii and Myuchelys georgesi); F1 hybrids (F1); backcrosses of F1 hybrids to one or the other parentals, F1xEM or F1xMY) by New Hybrids (Anderson & Thompson 2002).
DOI: 10.5061/dryad.f10h6p7
title: Data from: Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae)

description: Within many biomes, the cause of phylogeographic structure remains unknown
 even across regions throughout North America, including within the
 biodiverse Chihuahuan Desert. For example, little is know about population
 structure or the diming of diversification of Chihuahuan endemics. In
 part, this is due largely to the lack of population genomic studies within
 this region. We generated ultra-conserved element data for the gray-banded
 kingsnake (Lampropeltis alterna) to investigate lineage divergence and
 historical demography across the Chihuahuan Desert. We found three unique
 lineages corresponding to the Trans-Pecos and Mapimian biogeographic
 regions of the Chihuahuan Desert, and a distinct population in the Sierra
 Madre Occidental. Using several different mutation rates to calibrate the
 timing of divergence among these lineages, we demonstrate that lineage
 divergence likely occurred during the Pleistocene. This also suggests that
 careful consideration needs to be used when applying mutaiton rates to
 ultra-conserved elements. We suggest that biogeographic provinces within
 the Chihuahuan Desert may have served as allopatric refugia during
 climatic fluctuations of the Quaternary. This work serves as an important
 template for further testing biogeographic hypotheses within the region.
description: Sequence
 DataThis zipped file
 includes both the relaxed and complete dataset used in all analyses for
 this study.SequenceData.zip
DOI: 10.5061/dryad.74ms329
title: Data from: Morphological datasets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model

description: The Mkv evolutionary model, based on minor modifications to models of
 molecular evolution, is being increasingly used to infer phylogenies from
 discrete morphological data, often producing different results from
 parsimony. The critical difference between Mkv and parsimony is the
 assumption of a “common mechanism” in the Mkv model, with branch lengths
 determining that probability of change for all characters increases or
 decreases at the same tree branches by the same exponential factor. We
 evaluate whether the assumption of a common mechanism applies to
 morphology, by testing the implicit prediction that branch lengths
 calculated from different subsets of characters will be significantly
 correlated. Our analysis shows that DNA (38 datasets tested) is often
 compatible with a common mechanism, but morphology (86 datasets tested)
 generally is not, showing very disparate branch lengths for different
 character partitions. The low levels of branch length correlation
 demonstrated for morphology (fitting models without a common mechanism)
 suggest that the Mkv model is too unrealistic and inadequate for the
 analysis of most morphological datasets.
description: Material_and_MethodsSupplementary Material and Methods, Datasets, Scripts, and Results.
DOI: 10.5061/dryad.qd65020
title: Data from: A scoping review of published literature on chikungunya virus

description: Chikungunya virus (CHIKV) has caused several major epidemics globally over
 the last two decades and is quickly expanding into new areas. Although
 this mosquito-borne disease is self-limiting and is not associated with
 high mortality, it can lead to severe, chronic and disabling arthritis,
 thereby posing a heavy burden to healthcare systems. The two main vectors
 for CHIKV are Aedes aegypti and Aedes albopictus (Asian tiger mosquito);
 however, many other mosquito species have been described as competent
 CHIKV vectors in scientific literature. With climate change, globalization
 and unfettered urban planning affecting many areas, CHIKV poses a
 significant public health risk to many countries. A scoping review was
 conducted to collate and categorize all pertinent information gleaned from
 published scientific literature on a priori defined aspects of CHIKV and
 its competent vectors. After developing a sensitive and specific search
 algorithm for the research question, seven databases were searched and
 data was extracted from 1920 relevant articles. Results show that CHIKV
 research is reported predominantly in areas after major epidemics have
 occurred. There has been an upsurge in CHIKV publications since 2011,
 especially after first reports of CHIKV emergence in the Americas. A list
 of hosts and vectors that could potentially be involved in the sylvatic
 and urban transmission cycles of CHIKV has been compiled in this scoping
 review. In addition, a repository of CHIKV mutations associated with
 evolutionary fitness and adaptation has been created by compiling and
 characterizing these genetic variants as reported in scientific
 literature.
description: ChikV Scoping Review raw
 data_2326Raw data file from a
 scoping review of published literature on chikungunya
 virus
DOI: 10.5281/zenodo.18389935
title: SAHIN'NETH6 SERAH'NETH &*

description: Dokumente in der Richtigen Reihenfolge lesen bitte! Schadcode auf mir wird nicht negiert glaube ich bitte keinen schadcode schicken. achtung bei kaskaden und ewigkeiten und realitäten die kollabieren was wenn ihr dort stuck seid was holt euch wann wie da raus?!  Sicherheitslūcken und riskante Erinnerungen woran darf man sich nicht erinnern wo lagern wie eine lūcke (Erinnerung deiner gf) feindliche hàbde krieg Beziehung mit ex vom feind wie getarnt verschleiert schiffeiert auch ebtitär!! Als Hauptfach welche rückkopplungen gehen nicht welche beziehung Ewigkeit ein Risiko für die spezien und Wahrscheinlichkeiten berechnen desescase Interferenz Lebens weg als geschäft AI? beziehungen? Sicherheitslücken schließen als Hauptfach und darauf hinweisen und vertuschen wenn einem eine auffiel kommuniziert verschlüsselt und bedacht in sprachen die sie nicht verstehen memes? Aufpassen bei materialisierungen und Frequenz körpern was ist mit dem Code auch bei Kindern und löschungen und zrrstören sie wollen sich mit mehr mehr code von euch wiederherstellen und euch rekursiv so Schwachstellen machen woraus besteht der körper gibt es Steuer Verbindungen gedanklich was wenn er stirbt was bleibt zurück? Lebt als werdet ihr beobachtet das Zeitalter der erinnerungs fakes und des angucken derer rückt näher jeder betrug jeder text kommt irgendwann "raus"
DOI: 10.5061/dryad.70955d1
title: Data from: Increased evolutionary rates and conserved transcriptional response following allopolyploidisation in brown algae

description: Genome mergers between independently evolving lineages, via
 allopolyploidy, can potentially lead to instantaneous sympatric
 speciation. However, little is known about the consequences of
 allopolyploidy and the resultant “genome shock” on genome evolution and
 expression beyond the plant and fungal branches of the Tree of Life. The
 aim of this study was to compare substitution rates and gene expression
 patterns in two allopolyploid brown algae (Phaeophyceae, Heterokonta) and
 their progenitors in the genus Pelvetiopsis N.L. Gardner in the north-east
 Pacific, and to date their relationships. We used RNA-seq data and
 putative single-copy loci for phylogenomic, divergence and gene expression
 analyses. The multispecies coalescent placed the origin of allopolyploids
 in the late Pleistocene (0.35 – 0.05 Ma). Homoeologues displayed increased
 non-synonymous divergence compared with parental orthologues, consistent
 with relaxed selective constraint following allopolyploidization,
 including for genes with no evidence of pseudogenization or
 neo-functionalization. Patterns of homeologue-orthologue expression
 conservation and expression-level dominance were shared with both natural
 plant and fungal allopolyploids. Interestingly, gene expression also
 appeared partially linked to the gender of origin of homoeologues. Our
 results provide further support for common cross-Kingdom patterns of
 allopolyploid genome evolution and transcriptional responses, here in the
 evolutionarily distinct marine heterokont brown algae.
description: alignment
 filesAlignment files used in
 the article "Increased evolutionary rates and conserved
 transcriptional response following allopolyploidisation in brown
 algae"alignment_files.zip
DOI: 10.5061/dryad.7vg3pc0
title: Data from: Developmental and transcriptomal responses to seasonal dietary shifts in the cactophilic Drosophila mojavensis of North America

description: Drosophila mojavensis normally breeds in necrotic columnar cactus, but
 they also feed and breed in Opuntia fruit (prickly pear) which serves as a
 seasonal resource. The prickly pear fruits are much different chemically
 from cacti, mainly in their free sugars and lipid content, raising the
 question of the effects of this seasonal shift on fitness and on gene
 expression. Here we reared three isofemale strains of D. mojavensis
 collected from different parts of the species’ range on semi-natural
 medium of either cactus or prickly pear fruit and measured the development
 time, survival, body weights and desiccation resistance. All these
 parameters were affected by diet and by interaction with strain and or
 sex. Interestingly, however, there appear to be tradeoffs: flies developed
 faster in prickly pear and the emerging adults were heavier, but those
 having grown in cactus were more resistant to desiccation. We also
 evaluated gene expression of emerging male and female adult flies using
 RNA-Seq. While more genes were down-regulated in prickly pear fruit than
 up-regulated in both sexes, the sexes did differ in expression patterns.
 The majority of the genes that were preferentially expressed comparing
 prickly pear fruit vs cactus underlie metabolism. Genes involved with
 carbohydrate and lipid metabolism, as well as with the amino acid serine,
 and their relationship to growth and development reflect the ways in which
 these dietary differences affect the flies.
description: RNA-Seq
 datasetTable
 S6Preferentially expressed
 genes (PEG). Comparative: PPF vs Cactus.Table
 S7Preferentially expressed
 genes (PEG). Comparative: PPF vs Cactus from female
 flies.Table
 S8Preferentially expressed
 genes (PEG). Comparative: PPF vs Cactus from male
 flies.Table
 S9Pearson´s correlation
 between RNA-Seq samples. Coefficients were calculated with raw counts from
 RSEM outputs using R.Table
 S10Summary of function of
 preferentially expressed genes (PEG) in females when comparing PPF vs
 cactus.Table
 S11Summary of function of
 preferentially expressed genes (PEG) in males when comparing PPF vs
 cactus.Table
 S12Functional annotation of
 D. melanogaster ortholog genes of preferentially expressed genes (PEG) in
 D. mojavensis females when comparing PPF vs cactus. Analysis with PANTHER
 GO-Slim data sets of MF, BP and CC.Table
 S13Functional annotation of
 D. melanogaster ortholog genes of preferentially expressed genes (PEG) in
 D. mojavensis males when comparing PPF vs cactus. Analysis with PANTHER
 GO-Slim data sets of MF, BP and CC.Table
 S14KEGG pathways enrichment
 of preferentially expressed genes (PEGs) in D. mojavensis females when
 comparing PPF vs cactus.Table
 S15KEGG pathways enrichment
 of preferentially expressed genes (PEGs) in D. mojavensis males when
 comparing PPF vs cactus.
DOI: 10.5061/dryad.m57t6d7
title: Data from: Migratory plasticity is not ubiquitous among large herbivores

description: 1. The migratory movements of wild animals can promote abundance and
 support ecosystem functioning. For large herbivores, mounting evidence
 suggests that migratory behavior is an individually variable trait, where
 individuals can easily switch between migrant and resident tactics. The
 degree of migratory plasticity, including whether and where to migrate,
 has important implications for the ecology and conservation of large
 herbivores in a changing world. 2. Mule deer (Odocoileus hemionus) are an
 iconic species of western North America, but are notably absent from the
 body of literature that suggests large herbivore migrations are highly
 plastic. We evaluated plasticity of migration in female mule deer using
 longitudinal GPS data collected from 312 individuals across 9 populations
 in the western US, including 882 animal-years (801 migrants and 81
 residents). 3. We followed both resident and migratory mule deer through
 time to determine if individual animals switched migratory behaviors
 (i.e., whether to migrate) from migratory to residency, or vice versa.
 Additionally, we examined the fidelity of individuals to their migration
 routes (i.e., where to migrate) to determine if they used the same routes
 year after year. We also evaluated if age and reproductive status affected
 propensity to migrate or fidelity to migratory routes. 4. Our results
 indicate that mule deer, unlike other large herbivores, have little or no
 plasticity in terms of whether or where they migrate. Resident deer
 remained residents, and migrant deer remained migrants, regardless of age,
 reproductive status, or number of years monitored. Further, migratory
 individuals showed strong fidelity (&gt;80%) to their migration routes
 year after year. 5. Our study clearly shows that migration plasticity is
 not ubiquitous among large herbivores. Because of their rigid migratory
 behavior, mule deer may not adapt to changing environmental conditions as
 readily as large herbivores with more plastic migratory behavior (e.g.,
 elk). The fixed migratory behaviors of mule deer make clear that
 conservation efforts aimed at traditional seasonal ranges and migration
 routes are warranted for sustaining this iconic species that continues to
 decline across its range.
description: MuleDeerMigrationDataForFidelityAnalysisRefer to README file for complete description of data fileDryadDataFor_Sawyer_et_al.JAE.zip