cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t9r0
title: Data from: How do cuticular hydrocarbons evolve? Physiological constraints and climatic and biotic selection pressures act on a complex functional trait

description: Cuticular hydrocarbons (CHCs) cover the cuticles of virtually all insects,
 serving as a waterproofing agent and as a communication signal. The causes
 for the high CHC variation between species, and the factors influencing
 CHC profiles, are scarcely understood. Here, we compare CHC profiles of
 ant species from seven biogeographic regions, searching for physiological
 constraints and for climatic and biotic selection pressures. Molecule
 length constrained CHC composition: long-chain profiles contained fewer
 linear alkanes, but more hydrocarbons with disruptive features in the
 molecule. This is probably owing to selection on the physiology to build a
 semi-fluid cuticular layer, which is necessary for waterproofing and
 communication. CHC composition also depended on the precipitation in the
 ants' habitats. Species from wet climates had more alkenes and fewer
 dimethyl alkanes than those from drier habitats, which can be explained by
 different waterproofing capacities of these compounds. By contrast,
 temperature did not affect CHC composition. Mutualistically associated
 (parabiotic) species possessed profiles highly distinct from
 non-associated species. Our study is, to our knowledge, the first to show
 systematic impacts of physiological, climatic and biotic factors on
 quantitative CHC composition across a global, multi-species dataset. We
 demonstrate how they jointly shape CHC profiles, and advance our
 understanding of the evolution of this complex functional trait in
 insects.
description: Menzel et al Raw
 dataCuticular hydrocarbon
 data of the species investigated. In the first data sheet, each row is one
 CHC peak. The table contains information about the chain length, substance
 class, per cent abundance and methyl groups (if applicable). The second
 sheet contains information about the species collected, their phylogenetic
 affiliation, the latitude, annual precipitation and annual temperature of
 the collection site.
DOI: 10.5061/dryad.7fj2hd2
title: Data from: Which tools to use? choice optimization in the tool-using ant, Aphaenogaster subterranea

description: When encountering liquid food sources, ants of the genus Aphaenogaster
 drop various materials as tools into the food, and then carry the
 food-soaked tools back to the nest. Although this is one of the most
 well-documented examples of tool use in insects, we know little about
 which factors influence their choice of tools during foraging. Here, we
 investigated the tool-using behavior of Aphaenogaster subterranea by
 examining, across a range of settings, how tool-using workers deal with
 various foraging challenges. We used different types of tools and liquid
 baits with varying distances between the baits and the tools piled around
 them. Although ants showed the strongest preference for the most easily
 transportable tools, the frequency of usage of the less preferred larger
 tools increased when these were the first to be discovered or were more
 readily accessible to the ants. Additionally, tool selection occurred at
 two stages: when tools were picked up and dropped into baits, and later,
 when food-soaked tools were retrieved from baits. Our results confirm that
 tool use in A. subterranea exhibits a high degree of flexibility. Ants
 seem to be able not only to optimize their foraging effort by selecting
 tools that are best matched to the particular foraging environment, but
 also to learn how to improve the use of certain tools by modifying them.
 The adaptive value of flexibility in tool use may be the increased
 efficiency in the utilization of liquid food sources, which gains
 importance in the light of competition with co-occurring ant species.
description: Data for tool use of
 Aphaenogaster subterraneaevents: number of tools
 dropped into baits/carried from baits; tools: 1-small soil grains, 2-large
 soil grains, 3-pine needles, 4-leaves, 5-sponges; baits: 1-water,
 2-honey-water, 3-honey; distances: 1-4 cm, 2-12 cmdata.xlsx
DOI: 10.5061/dryad.8s3p0
title: Data from: Importance of latrine communication in European rabbits shifts along a rural–to–urban gradient

description: BACKGROUND: Information transfer in mammalian communication networks is
 often based on the deposition of excreta in latrines. Depending on the
 intended receiver(s), latrines are either formed at territorial boundaries
 (between-group communication) or in core areas of home ranges
 (within-group communication). The relative importance of both types of
 marking behavior should depend, amongst other factors, on population
 densities and social group sizes, which tend to differ between urban and
 rural wildlife populations. Our study is the first to assess (direct and
 indirect) anthropogenic influences on mammalian latrine-based
 communication networks along a rural-to-urban gradient in European rabbits
 (Oryctolagus cuniculus) living in urban, suburban and rural areas in and
 around Frankfurt am Main (Germany). RESULTS: The proportion of latrines
 located in close proximity to the burrow was higher at rural study sites
 compared to urban and suburban ones. At rural sites, we found the largest
 latrines and highest latrine densities close to the burrow, suggesting
 that core marking prevailed. By contrast, latrine dimensions and densities
 increased with increasing distance from the burrow in urban and suburban
 populations, suggesting a higher importance of peripheral marking.
 CONCLUSIONS: Increased population densities, but smaller social group
 sizes in urban rabbit populations may lead to an increased importance of
 between-group communication and thus, favor peripheral over core marking.
 Our study provides novel insights into the manifold ways by which man-made
 habitat alterations along a rural-to-urban gradient directly and
 indirectly affect wildlife populations, including latrine-based
 communication networks.
description: Ziege et al. 2016 Field
 data latrine surveySheet 1 (Latrine data):
 Data gained from systematically mapping latrines by two persons walking
 line transects (app. 5 m apart) across the entire study area within 15
 different study sites. Data was collected in the early morning during the
 reproductive season of rabbits in 2011 (April to September). Sheet 2
 (Calculation degree of urbanity): Data stemming from transect counts
 within study sites (visitors per min and ha), the Einwohnermeldeamt of
 Frankfurt (residents within 500 m) and the use of ArcGis and map material
 provided by the city of Frankfurt (percent sealed surface and numbers of
 anthropogenic objects). Data on rabbit/burrow densities and group sizes
 respectively have been gained through observation at burrows and the use
 of ferrets that chased rabbits out of their burrow.Ziege et al 2016 Field data
 latrine survey.xls
DOI: 10.15482/usda.adc/28535408
title: Data from: Strategies for mitigating greenhouse gas emissions from US dairy farms toward a net zero goal

description: Representative dairy farms in major dairy regions of the United States were modeled using the Integrated Farm System Model to quantify potential reductions in greenhouse gas emissions using various mitigation strategies. Important data and information describing these 14 farms are documented in this table. These data include the farm location, number of cows and heifers maintained, milk produced, feeds and nutrient contents fed, crop areas, crop yields, fertilizer and lime application rates, irrigation water applied, milking and housing facilities, manure collection, storage and application methods used, and soil characteristics. Simulated output information for feed consumption, nutrient losses, fossil energy use, water use, and greenhouse gas emissions are listed for each farm. These data are published as supplementary information for the article “Strategies for mitigating greenhouse gas emissions from US dairy farms toward a net zero goal” published in the Journal of Dairy Science.
DOI: 10.15482/usda.adc/28535408.v1
title: Data from: Strategies for mitigating greenhouse gas emissions from US dairy farms toward a net zero goal

description: Representative dairy farms in major dairy regions of the United States were modeled using the Integrated Farm System Model to quantify potential reductions in greenhouse gas emissions using various mitigation strategies. Important data and information describing these 14 farms are documented in this table. These data include the farm location, number of cows and heifers maintained, milk produced, feeds and nutrient contents fed, crop areas, crop yields, fertilizer and lime application rates, irrigation water applied, milking and housing facilities, manure collection, storage and application methods used, and soil characteristics. Simulated output information for feed consumption, nutrient losses, fossil energy use, water use, and greenhouse gas emissions are listed for each farm. These data are published as supplementary information for the article “Strategies for mitigating greenhouse gas emissions from US dairy farms toward a net zero goal” published in the Journal of Dairy Science.
DOI: 10.15468/f636b4
title: Camellia shangshii (Theaceae), a new species endemic to danxia landscape from Guangdong Province, China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Wang, Shiyang, Liu, Hua, Tan, Shimin, Shen, Liran, Chen, Zaixiong, Chen, Fang, Fan, Qiang (2026): Camellia shangshii (Theaceae), a new species endemic to danxia landscape from Guangdong Province, China. PhytoKeys 270: 13-23, DOI: 10.3897/phytokeys.270.172597AbstractCamellia shangshii, a new species discovered in the danxia landscape of Danxiashan Mountain, Guangdong Province, China, is formally described and illustrated here. Morphologically, C. shangshii is similar to C. grijsii but can be distinguished by its petals connate at the base, smaller leaves, and fewer bracteoles and sepals. Phylogenetic analysis based on chloroplast genomes indicated that C. shangshii is a sister species to C. grijsii. By integrating morphological and molecular data, we validate the recognition of C. shangshii as a new species of C. sect. Paracamellia.
DOI: 10.5061/dryad.764h1
title: Data from: Sex-specific, inverted rhythms of breeding-site attendance in an Arctic seabird

description: In contrast to daily rhythms that are common in the presence of the
 geophysical light–dark cycle, organisms at polar latitudes exhibit many
 diel activity patterns during natural periods of continuous solar light or
 darkness (polar day and night, respectively), from 24 h rhythms to
 arrhythmicity. In Arctic Greenland (73.7° N, 56.6° W) during polar day, we
 observed breeding-site attendance rhythms of thick-billed murres (Uria
 lomvia; n = 21 pairs), a charadriiform seabird, which provide biparental
 care at the colony. We found that U. lomvia egg-incubation and
 chick-brooding attendance is rhythmic and synchronized to the geophysical
 day (mean period length [rhythm duration] ± 95% confidence interval =
 24.13 ± 0.52 h). Individual pair members had temporally segregated,
 sex-specific colony-attendance rhythms that were opposite (inverted) to
 each other, and these sex-specific rhythms were prominent at the
 population level. Our results provide a basis for investigating circadian
 systems at polar latitudes and sex-specific parental-care strategies.
description: On-duty Attendance
 DataEgg-incubating and
 chick-brooding attendance data recorded as bird-mins/h.OnDuty_Att.csvOff-duty Attendance DataData recorded as bird-mins/h for when an individual is attending the breeding site when their mate is incubating or brooding.OffDuty_Att.csvTotal Attendance DataData recorded as bird-mins/h for all of an individual's attendance at the breeding site.Total_Att.csvR CodeR code used for data manipulation and analysesRcode.rtf
DOI: 10.5061/dryad.fs348
title: Data from: Invasion of two tick-borne diseases across New England: harnessing human surveillance data to capture underlying ecological invasion processes

description: Modelling the spatial spread of vector-borne zoonotic pathogens maintained
 in enzootic transmission cycles remains a major challenge. The best
 available spatio-temporal data on pathogen spread often take the form of
 human disease surveillance data. By applying a classic ecological
 approach—occupancy modelling—to an epidemiological question of disease
 spread, we used surveillance data to examine the latent ecological
 invasion of tick-borne pathogens. Over the last half-century, previously
 undescribed tick-borne pathogens including the agents of Lyme disease and
 human babesiosis have rapidly spread across the northeast United States.
 Despite their epidemiological importance, the mechanisms of tick-borne
 pathogen invasion and drivers underlying the distinct invasion
 trajectories of the co-vectored pathogens remain unresolved. Our approach
 allowed us to estimate the unobserved ecological processes underlying
 pathogen spread while accounting for imperfect detection of human cases.
 Our model predicts that tick-borne diseases spread in a diffusion-like
 manner with occasional long-distance dispersal and that babesiosis spread
 exhibits strong dependence on Lyme disease.
description: Tick-borne disease
 surveillance dataTown-level Lyme disease
 and babesiosis surveillance data for Connecticut, Rhode Island, and
 Massachusetts. Case numbers are redacted for any town reporting &lt;5
 cases in a given year. NAs indicate years in which no surveillance data
 was available (see Table S1).tbdRawData.csv
DOI: 10.5061/dryad.889h8
title: Data from: A 20-year investigation of declining leatherback hatching success: implications of climate variation

description: Unprecedented increases in air temperature and erratic precipitation
 patterns are predicted throughout the 21st century as a result of climate
 change. A recent global analysis of leatherback turtle hatchling output
 predicts that the nesting site at Sandy Point National Wildlife Refuge
 (SPNWR) will experience the most significant regional climate alterations.
 We aimed to identify how local air temperatures and precipitation patterns
 influenced within nest mortality and overall hatchling output at this site
 between 1990 – 2010. We show that while the greatest mortality occurred
 during the latest stages of development (stage three), the rate of embryo
 mortality was highest during the initial stages (stage zero) of
 development (~3.8 embryos/day/clutch). Increased mortality at stage three
 was associated with decreased precipitation and increased temperature
 during this developmental period, whereas precipitation prior to, and
 during stage zero had the greatest influence on early mortality. There was
 a significant decline in overall hatching success (falling from 74% to
 55%) and emergence rate (calculated from the number of hatchlings that
 emerged from the nest as a percentage of hatched eggs) which fell from 96%
 to 91%, However, there was no trend observed in local temperature or
 precipitation during this timeframe, and neither variable was related to
 hatching success or emergence rate. In conclusion, our findings suggest
 that despite influencing within-nest mortality, climatic variability does
 not account for the overall decline in hatchling output at SPNWR from 1990
 – 2010. Further research is therefore needed to elicit the reasons for
 this decline.
description: Dryad_StCroix_04032017Each line represents a nest; Temperature measurements are in degrees celcius (mean); Precipitation measurements are in mm (accumulated); mortality data (at each stage, hatching and emergence rate) are percentage of overall clutch.
DOI: 10.5061/dryad.5km4m
title: Data from: Development of a Chinook salmon sex identification SNP assay based on the growth hormone pseudogene

description: Genotypic sex identification assays can provide valuable information about
 fish populations when phenotypic sex determination is difficult. Here we
 describe the development of a TaqMan® assay (Ots_SexID) designed to
 identify the genotypic sex of Winter-Run Chinook salmon collected from the
 Sacramento River and spawned at the Livingston Stone National Fish
 Hatchery. The TaqMan® assay targets a region previously examined in the
 growth hormone pseudogene. Accuracy of the marker was assessed by
 comparing genotypic sex assignments for Chinook salmon spawned at
 Livingston Stone National Fish hatchery in 2012 (n = 84) to phenotypic sex
 recorded during spawning. Genotypic sex was observed to be concordant with
 phenotypic sex identified using Ots_SexID in 83/84 individuals, suggesting
 that the assay could be used to predict phenotypic sex with ~99% accuracy.
 To evaluate the utility of the TaqMan® assay in other parts of the
 species' range, we examined collections from 29 other populations
 ranging from Alaska to California. Sex assignments based on the assay were
 generally concordant with observed phenotypes, but there were some strong
 exceptions. These results suggest that the new assay will be very useful
 in Sacramento River Winter-Run Chinook salmon, but also highlight the
 importance of thoroughly testing any sex identification assay prior to
 application in a population of interest.
description: Table
 S1Phenotypic and genotypic
 sex assignment of Winter-Run Chinook salmon (Oncorhynchus tshawytscha)
 spawned at Livingston Stone National Fish Hatchery in 2012. Phenotypic sex
 assignment was made during spawning. Genotypic sex assignments were made
 using a fragment-based assay and also using the novel TaqMan® assay,
 Ots_SexID. Samples for which phenotypic and genotypic sex assignment
 conflicted are indicated in bold font.Reference
 S1Baumsteiger, JD, Niemela
 KS, Null RE, Ardren WR. 2005. The Inclusion of Sexually-Determinate
 Molecular Markers into the Broodstock Selection Protocol for Winter-Run
 Chinook salmon at Livingston Stone National Fish Hatchery. AFTC
 Report.Baumsteiger et al.
 2005.pdfReference
 S2Von
 Bargen J, Smith CT. 2013. Genetic identification of endangered winter-run
 Chinook salmon in the Sacramento River, CA, AFTC Final Report
 FY2012.LSNFH FY2012 Final
 Report.pdf
DOI: 10.5061/dryad.f4r38
title: Data from: Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects

description: Background Body plan development in multi-cellular organisms is largely
 determined by homeotic genes. Expression of homeotic genes, in turn, is
 partially regulated by insulator binding proteins (IBPs). While only a few
 enhancer blocking IBPs have been identified in vertebrates, the common
 fruit fly Drosophila melanogaster harbors at least twelve different
 enhancer blocking IBPs. We screened recently compiled insect
 transcriptomes from the 1KITE project and genomic and transcriptomic data
 from public databases, aiming to trace the origin of IBPs in insects and
 other arthropods. Results Our study shows that the last common ancestor of
 insects (Hexapoda) already possessed a substantial number of IBPs.
 Specifically, of the known twelve insect IBPs, at least three (i.e.,
 CP190, Su(Hw), and CTCF) already existed prior to the evolution of
 insects. Furthermore we found GAF orthologs in early branching insect
 orders, including Zygentoma (silverfish and firebrats) and Diplura
 (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of
 Neoptera, while Pita is likely an evolutionary novelty of holometabolous
 insects. Zw5 appears to be restricted to schizophoran flies, whereas
 BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus
 Drosophila. Selection models indicate that insect IBPs evolved under
 neutral or purifying selection. Conclusions Our results suggest that a
 substantial number of IBPs either pre-date the evolution of insects or
 evolved early during insect evolution. This suggests an evolutionary
 history of insulator binding proteins in insects different to that
 previously thought. Moreover, our study demonstrates the versatility of
 the 1KITE transcriptomic data for comparative analyses in insects and
 other arthropods.
description: Amino acid alignments of
 insect insulator proteinsThis archive contains
 amino acid alignments of all insect insulator proteins found in the 1KITE
 transcriptome data and the sequences that were used, to infer profile
 Hidden Markov Models for this search. The alignments are in the .fasta
 file format.insulator_proteins_amino_acid_alignments.tar.gzGene trees of insect insulator proteinsThis archive contains all gene trees inferred from amino acid alignments of insulator protein sequences that were found in the 1KITE transcriptome data. The gene trees are in the .newick file format.insulator_proteins_gene_trees.tar.gzNucleotide alignments of insect insulator proteinsThis archive contains all nucleotide alignments of insect insulator protein sequences found in the 1KITE project. These alignments have been used to infer dN/dS ratios as markers for positive or negative selection in these sequences. The alignments are in the .fasta file format.insulator_proteins_nucleotide_alignments.tar.gz
DOI: 10.5061/dryad.12g3c7ht
title: Data from: Pervasive genetic integration directs the evolution of human skull shape

description: It has long been unclear whether the different derived cranial traits of
 modern humans evolved independently in response to separate selection
 pressures or whether they resulted from the inherent morphological
 integration throughout the skull. In a novel approach to this issue, we
 combine evolutionary quantitative genetics and geometric morphometrics to
 analyze genetic and phenotypic integration in human skull shape. We
 measured human skulls in the ossuary of Hallstatt (Austria), which offer a
 unique opportunity because they are associated with genealogical data. Our
 results indicate pronounced covariation of traits throughout the skull.
 Separate simulations of selection for localized shape changes
 corresponding to some of the principal derived characters of modern human
 skulls produced outcomes that were similar to each other and involved a
 joint response in all of these traits. The data for both genetic and
 phenotypic shape variation were not consistent with the hypothesis that
 the face, cranial base and cranial vault are completely independent
 modules but relatively strongly integrated structures. These results
 indicate pervasive integration in the human skull and suggest a
 reinterpretation of the selective scenario for human evolution where the
 origin of any one of the derived characters may have facilitated the
 evolution of the others.
description: G_matrixAdditive genetic variance-covariance square matrix for skull shape.P_matrixPhenotypic genetic variance-covariance square matrix for skull shape.