cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8bf48
title: Data from: Genomic diversity and differentiation of a managed island wild boar population

description: The evolution of island populations in natural systems is driven by local
 adaptation and genetic drift. However, evolutionary pathways may be
 altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an
 iconic game species occurring in several islands, where it has been
 strongly managed since prehistoric times. We examined genomic diversity at
 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared
 them with 196 wild specimens from mainland Europe and 105 domestic pigs
 (DP; 11 breeds). High levels of genetic variation were observed in
 Sardinia (80.9% of the total number of polymorphisms), which can be only
 in part associated to recent genetic introgression. Both Principal
 Component Analysis and Bayesian clustering approach revealed that the
 Sardinian WB population is highly differentiated from the other European
 populations (FST=0.126–0.138), and from DP (FST=0.169). Such evidences
 were mostly unaffected by an uneven sample size, although clustering
 results in reference populations changed when the number of individuals
 was standardized. Runs of homozygosity (ROHs) pattern and distribution in
 Sardinian WB are consistent with a past expansion following a bottleneck
 (small ROHs) and recent population substructuring (highly homozygous
 individuals). The observed effect of a non-random selection of Sardinian
 individuals on diversity, FST and ROH estimates, stressed the importance
 of sampling design in the study of structured or introgressed populations.
 Our results support the heterogeneity and distinctiveness of the Sardinian
 population and prompt further investigations on its origins and
 conservation status.
description: WB_DP_pedped file with WB and DP individualsLI_WB_DP.pedWB_DP_mapmap file associated with the ped fileLI_WB_DP.mapWB_DP_structure_infileStructure input file. The four populations correspond to the "Group" column in the file Individuals_info.txtLI_WB_DP.struIndividuals_infoAdditional information on the individuals analysedREADME
DOI: 10.5061/dryad.62j0q
title: Data from: Identification of glucose kinase dependent and independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics

description: Members of the soil-dwelling prokaryotic genus Streptomyces are
 indispensable for the recycling of complex polysaccharides, and produce a
 wide range of natural products. Nutrient availability is a major
 determinant for the switch to development and antibiotic production in
 streptomycetes. Carbon catabolite repression (CCR), a main signaling
 pathway underlying this phenomenon, was so far considered fully dependent
 on the glycolytic enzyme glucose kinase (Glk). Here we provide evidence of
 a novel Glk-independent pathway in Streptomyces coelicolor, using advanced
 proteomics that allowed the comparison of the expression of some 2,000
 proteins, including virtually all enzymes for central metabolism. While
 CCR and inducer exclusion of enzymes for primary and secondary metabolism
 and precursor supply for natural products is mostly mediated via Glk,
 enzymes for the urea cycle, as well as for biosynthesis of the
 γ-butyrolactone Scb1 and the responsive cryptic polyketide Cpk are subject
 to Glk-independent CCR. Deletion of glkA led to strong downregulation of
 biosynthetic proteins for prodigionin and calcium-dependent antibiotic
 (CDA) in mannitol-grown cultures. Repression of bldB, bldN, and its target
 bldM explains the poor development of S. coelicolor on solid-grown
 cultures containing glucose. A new model for carbon catabolite repression
 in streptomycetes is presented.
description: Quantitative proteomics
 data setThe folder
 'Mannitol' contains data from the two mixtures (M1, M2) in the
 mannitol background. The folder 'Fructose' contains data from
 the two mixtures (M1, M2) in the fructose background. Mixtures were
 prepared as shown in Fig. 1a of the main paper: | Label: Strain, Carbon
 source (X = fructose or mannitol) | M1: | Light (L): M145, G+X | Medium
 (M): M145, X | Heavy (H): dGlkA, G+X | M2: | Light (L): dGlkA, X | Medium
 (M): M145, X | Heavy (H): dGlkA, G+X | Normalized ratios as found in
 proteinGroups.txt were used to create the data tables in the main paper.
 Descriptions of all tables and column headers can be found in
 'tables.pdf'. All tables were created using MaxQuant
 1.2.2.5.glka_proteomics.zip
DOI: 10.5061/dryad.7137r
title: Data from: Horizontal transmission of the father’s song in the Zebra Finch (Taeniopygia guttata)

description: As is the case for human speech, birdsong is transmitted across
 generations by imitative learning. Although transfer of song patterns from
 adults to juveniles typically occurs via vertical or oblique transmission,
 there is also evidence of horizontal transmission between juveniles of the
 same generation. Here, we show that a young male zebra finch (Taeniopygia
 guttata) that has been exposed to its father during the sensitive period
 for song learning can lead a brother, that has never heard the paternal
 song, to imitate some sounds of the father. Moreover, song similarity
 between the two brothers was higher than the similarity measured between
 the paternal song and the song of the brother that had a week-long
 exposure to the father. We speculate that the phenomenon of
 within-generation song learning among juveniles may be more widespread
 than previously thought and that when a juvenile evaluates potential
 models for imitative learning, a sibling may be as salient as an adult.
description: bird1174_pair1_tutor_all_songssound filebird1363_pair1_son1_all_songsbird1362_pair1_son2_all_songsbird1214_pair2_tutor_all_songsbird1373_pair2_son1_all_songsbird1375_pair2_son2_all_songsbird165_pair3_tutor_all_songsbird1381_pair3_son1_all_songsbird1382_pair3_son2_all_songsbird657_pair4_tutor_all_songsbird1386_pair4_son1_all_songsbird1385_pair4_son2_all_songsbird1162_pair5_tutor_all_songsbird1398_pair5_son1_all_songssound filebird1394_pair5_son2_all_songsbird640_pair6_tutor_all_songsbird1402_pair6_son1_all_songsbird1401_pair6_son2_all_songssound filebird975_pair7_tutor_all_songssound filebird1419_pair7_son1_all_songssound filebird1418_pair7_son2_all_songsbird1170_pair8_tutor_all_songsbird1448_pair8_son1_all_songsbird1445_pair8_son2_all_songsbird1206_pair9_tutor_all_songsbird1451_pair9_son1_all_songsbird1449_pair9_son2_all_songs
DOI: 10.5061/dryad.05pr1n8
title: Data from: Genetics and genomics of an unusual selfish sex ratio distortion in an insect

description: Diverse selfish genetic elements have evolved the ability to manipulate
 reproduction to increase their transmission, and this can result in highly
 distorted sex ratios. Indeed, one of the major explanations for why sex
 determination systems are so dynamic is because they are shaped by ongoing
 coevolutionary arms races between sex ratio distorting elements and the
 rest of the genome. Here, we use genetic crosses and genome analysis to
 describe an unusual sex ratio distortion with striking consequences on
 genome organization in a booklouse species, Liposcelis sp. (Insecta:
 Psocodea), in which two types of females coexist. Distorter females never
 produce sons but must mate with males (the sons of nondistorting females)
 to reproduce. Although they are diploid and express the genes inherited
 from their fathers in somatic tissues, distorter females only ever
 transmit genes inherited from their mothers. As a result, distorter
 females have unusual chimeric genomes, with distorter-restricted
 chromosomes diverging from their nondistorting counterparts and exhibiting
 features of a giant nonrecombining sex chromosome. The
 distorter-restricted genome has also acquired a gene from the bacterium
 Wolbachia, a well-known insect reproductive manipulator; we found that
 this gene has independently colonized the genomes of two other insect
 species with unusual reproductive systems suggesting possible roles in sex
 ratio distortion in this remarkable genetic system.
description: Hamilton_etal_2018_Liposcelis_DataCompiled data from 'Genetics and genomics of an unusual selfish sex ratio distortion in an insect'. Contains seven files, including genome and transcriptome assemblies, as well as read mappings. See included outline for more details.Hamilton_etal_2018_Liposcelis.zip
DOI: 10.5061/dryad.b65fj
title: Data from: A new low-turbulence wind tunnel for animal and small vehicle flight experiments

description: Our understanding of animal flight benefits greatly from specialized wind
 tunnels designed for flying animals. Existing facilities can simulate
 laminar flow during straight, ascending and descending flight, as well as
 at different altitudes. However, the atmosphere in which animals fly is
 even more complex. Flow can be laminar and quiet at high altitudes but
 highly turbulent near the ground, and gusts can rapidly change wind speed.
 To study flight in both laminar and turbulent environments, a
 multi-purpose wind tunnel for studying animal and small vehicle flight was
 built at Stanford University. The tunnel is closed-circuit and can produce
 airspeeds up to 50 m s−1 in a rectangular test section that is 1.0 m wide,
 0.82 m tall and 1.73 m long. Seamless honeycomb and screens in the airline
 together with a carefully designed contraction reduce centreline
 turbulence intensities to less than or equal to 0.030% at all operating
 speeds. A large diameter fan and specialized acoustic treatment allow the
 tunnel to operate at low noise levels of 76.4 dB at 20 m s−1. To simulate
 high turbulence, an active turbulence grid can increase turbulence
 intensities up to 45%. Finally, an open jet configuration enables stereo
 high-speed fluoroscopy for studying musculoskeletal control in turbulent
 flow.
description: Wind Tunnel Aeroacoustic
 Testing DataThe uploaded
 aeroacoustic data were taken in the empty test section during wind tunnel
 commissioning. See the Wind Tunnel Data README file for details on file
 structure.QuinnEtAl_Data.zip
DOI: 10.5061/dryad.gm41t
title: Data from: A new species of Chiasmocleis (Microhylidae, Gastrophryninae) from the Atlantic Forest of Espírito Santo State, Brazil

description: Among Neotropical microhylids, the genus Chiasmocleis is exceptionally
 diverse. Most species of Chiasmocleis were described in recent years based
 on external morphology, but recent studies using molecular data did not
 support the monophyly of the species groups clustered based on feet
 webbing. Furthermore, a phylogeographic study of C. lacrimae estimated
 high genetic divergence and low gene flow among populations across small
 geographic ranges. Increasing the molecular and geographic sampling, and
 incorporating morphological data, we identified new cryptic species.
 Herein, we used novel genetic and morphological data to describe a new
 species of Chiasmocleis.
description: 12SAlignment of
 12S16SAlignment
 16SBDNFAlignmentND2Alignment ND2datamatrixConcatenated dataRAxML_infileRAxML input fileRAxMLRAxML treepartition_schemeBest partition scheme and substitution models chosen by Partition FinderBeast_50KInput file of BeastBeast_50KBeast treeBeast_50K.logBeast log fileBeast_50K.treesBeast trees
DOI: 10.5061/dryad.1212
title: Data from: Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms

description: A key issue concerning recovery from mass extinctions is how extinction
 and diversification mechanisms affect the recovery process. We evolved
 communities of digital organisms, subjecting them to instantaneous “pulse”
 extinctions, choosing survivors at random, or to prolonged “press”
 extinctions involving a period of low resource availability. Functional
 activity at low trophic levels recovered faster than at higher levels,
 with the most extensive delays seen at the top level. Postpress
 communities generally did not fully recover functional activity in the
 allotted time, which equaled that of their original diversification. We
 measured recovery of phenotypic diversity, observing considerable
 variation in outcomes. Communities subjected to pulse extinctions
 recovered functional activity and phenotypic diversity substantially
 faster than when subjected to press extinctions. Follow‐up experiments
 tested whether organisms with shorter generation times and low functional
 activity contributed to delayed recovery after press extinctions. The
 results indicate that adaptation during the press episode degraded the
 organisms’ ability to reevolve preextinction functionality. There are
 interesting parallels with patterns from the paleontological record. We
 suggest that some delayed recoveries from mass extinction may reflect the
 need to both reevolve biological functions and reconstruct ecological
 interactions lost during the extinction. Adaptation to conditions during
 an extended disturbance may hinder subsequent recovery.
description: AMNAT50172R2rawdata.tarRaw data for Am Nat 50172R2. TAR archive containing Excel spreadsheets with data used for figures in main text and supplementary material. All data generated by Avida digital evolution software. Spreadsheet files named with reference to the figure made with the data contained in that file.
DOI: 10.5061/dryad.60mk5
title: Data from: An indexed, mapped mutant library enables reverse genetics studies of biological processes in Chlamydomonas reinhardtii

description: The green alga Chlamydomonas reinhardtii is a leading single-celled model
 for dissecting biological processes in photosynthetic eukaryotes. However,
 its usefulness has been limited by difficulties in obtaining mutants in
 genes of interest. To allow generation of large numbers of mapped mutants,
 we developed high-throughput methods which: (1) Enable easy propagation on
 agar and cryogenic maintenance of tens of thousands of C. reinhardtii
 strains; (2) Identify mutant insertion sites and physical coordinates in
 such collections; (3) Validate the insertion sites in pools of mutants by
 obtaining &gt;500 bp of flanking genomic sequences. We used these
 approaches to construct a stably maintained library of 1,935 mapped
 mutants, representing disruptions in 1,562 genes. We further characterized
 randomly selected mutants, and found that 33 out of 44 insertion sites
 (75%) could be confirmed by PCR, and 17 out of 23 mutants (74%) contained
 a single insertion. To demonstrate the power of this library for
 elucidating biological processes, we analyzed the lipid content of mutants
 disrupted in genes encoding proteins of the algal lipid droplet proteome.
 This study revealed a central role of the long-chain acyl-CoA synthetase
 LCS2 in the production of triacylglycerol from de novo synthesized fatty
 acids.
description: Supplemental Data Set 1.
 Structural differences in the CC-4533 genome relative to reference and
 other strains.tpc00465_SupplementalDS1.xlsxSupplemental Data Set 2. High-confidence genomic differences unique to CC-4533.tpc00465_SupplementalDS2.xlsxSupplemental Data Set 3. Binary codes for plate super-pooling.tpc00465_SupplementalDS3.xlsbSupplemental Data Set 4. Binary codes for colony super-pooling.tpc00465_SupplementalDS4.xlsbSupplemental Data Set 5. Read counts of each flanking sequence in each super-pool.tpc00465_SupplementalDS5.xlsbSupplemental Data Set 6. Validation of flanking sequence deconvolution in randomly selected mutants.tpc00465_SupplementalDS6.xlsbSupplemental Data Set 7. Full library data: colony positions, insertion sites, deconvolution and LEAP-Seq summary, gene annotation.tpc00465_SupplementalDS7.xlsbSupplemental Data Set 8. LEAP-Seq read details for each flanking sequence.tpc00465_SupplementalDS8.txtSupplemental Data Set 9. Summary of PCR results to check the insertion sites of randomly-picked mutants from the mutant library.tpc00465_SupplementalDS9.xlsxSupplemental Data Set 10. Statistically significant insertion hotspots and coldspots.tpc00465_SupplementalDS10.xlsbSupplemental Data Set 11. Insertions in genes encoding lipid droplet proteins were characterized by PCR.tpc00465_SupplementalDS11.xlsx
DOI: 10.15468/dl.n6vtrs
title: Occurrence Download

description: A dataset containing 14711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Adinetidae, Brachionidae, Gastropodidae, Dicranophoridae, Asplanchnidae, Euchlanidae, Proalidae, Notommatidae, Philodinidae, Collothecidae, Lepadellidae, Conochilidae, Trichocercidae, Epiphanidae, Trochosphaeridae, Flosculariidae, Habrotrochidae, Hexarthridae, Ituridae, Lecanidae, Lindiidae, Mytilinidae, Trichotriidae, Microcodidae, Philodinavidae, Synchaetidae, Testudinellidae, Scaridiidae, Tetrasiphonidae, Centropagidae, Diaptomidae, Cyclopidae, Halicyclopidae, Lernaeidae, Canthocamptidae, Ameiridae, Laophontidae, Phyllognathopodidae, Miraciidae, Ergasilidae, Daphniidae, Moinidae, Bosminidae, Chydoridae, Macrothricidae, Ilyocryptidae, Neothricidae)",
 "Geometry POLYGON ((-181.131592 -37.12775, -187.78141 -33.078885, -189.068184 -33.987495, -186.411552 -37.925243, -192.774353 -44.251839, -195.387383 -46.345032, -192.379532 -48.31083, -188.062592 -45.989329, -183.377609 -41.69727, -180.416107 -38.542795, -181.131592 -37.12775))"
 ]
}

 The dataset includes 14711 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000408-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.917km
title: Data from: Mechanical evidence that flamingos can support their body on one leg with little active muscular force

description: Flamingos (Phoenicopteridae) often stand and sleep on one leg for long
 periods, but it is unknown how much active muscle contractile force they
 use for the mechanical demands of standing on one leg: body weight support
 and maintaining balance. First, we demonstrated that flamingo cadavers
 could passively support body weight on one leg without any muscle activity
 while adopting a stable, unchanging, joint posture resembling that seen in
 live flamingos. By contrast, the cadaveric flamingo could not be stably
 held in a two-legged pose, suggesting a greater necessity for active
 muscle force to stabilize two-legged versus one-legged postures. Our
 results suggest that flamingos engage a passively engaged gravitational
 stay apparatus (proximally located) for weight support during one-legged
 standing. Second, we discovered that live flamingos standing on one leg
 have markedly reduced body sway during quiescent versus alert behaviours,
 with the point of force application directly under the distal joint,
 reducing the need for muscular joint torque. Taken together, our results
 highlight the possibility that flamingos stand for long durations on one
 leg without exacting high muscular forces and, thus, with little energetic
 expenditure.
description: CadaverBirdDataThese are various data files from the cadaver experiment. Kinematics data taken from a cadaveric specimen, images from dissection of the pelvis (acetabulum and antitrochanter) and from museum specimens.LiveBirdDataThese are center of pressure data collected from force platform measurements on live Chilean flamingos (P. Chilensis) at Zoo Atlanta. Data files include spreadsheets of descriptions of trials, foot positions on force plate, Word text document describing trials analyzed, and a Matlab (.mat) file of some of the COP data analyzed.ExtraneousData_MyosinFiberTypesThis is a spreadsheet of data on myosin fiber types analyzed by a colleague, Dr. Thomas Burkholder, on muscles sampled from our cadaver specimens (P. Ruber) acquired from the Birmingham Zoo. Unfortunately, we did not have high confidence in the results due to the poor condition of tissue after multiple freeze/thaw cycles. We include them here, however, in the hopes that they may provide some insights.
DOI: 10.5061/dryad.9r3v1c3
title: Data from: Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill

description: Deep-sea coral communities are key components of the Gulf of Mexico
 ecosystem and were adversely affected by the Deepwater Horizon (DWH) oil
 spill. Coral colonies exposed to oil and dispersant exhibited mortality,
 damage, and physiological signatures of stress. Understanding how corals
 respond to oil and dispersant exposure at the molecular level is important
 to elucidate the sub-lethal effects of the DWH disaster, and reveal
 broader patterns of coral stress responses. Gene expression profiles from
 RNAseq data were compared between corals at an impacted site and from a
 reference site. A total of 1,439 differentially expressed genes (≥ 2-fold)
 were shared among impacted Paramuricea biscaya colonies. Genes involved in
 oxidative stress, immunity, wound repair, tissue regeneration, and
 metabolism of xenobiotics were significantly differentially expressed in
 impacted corals. Enrichment among the over-expressed genes indicates the
 corals were enduring high metabolic demands associated with cellular
 stress responses and repair mechanisms. Under-expression of genes vital to
 toxin processing also suggests a diminished capacity to cope with
 environmental stressors. Our results provide evidence that deep-sea corals
 exhibited genome-wide cellular stress responses to oil and dispersant
 exposure and demonstrate the utility of next-generation sequencing for
 monitoring anthropogenic impacts in deep waters. These analyses will
 facilitate the development of diagnostic markers for oil and dispersant
 exposure in deep-sea invertebrates and inform future oil spill response
 efforts.
description: Paramuricea biscaya
 reference transcriptomeTranscriptome assembly
 containing in situ preserved deep-sea octocorals; DWH spill impacted P.
 biscaya colonies and control P. biscaya colonies without visible signs of
 impact. mRNA library preparation was done via TruSeq RNA Library
 Preparation Kit at the University of Wisconsin-Madison Biotechnology
 Center and sequenced on an Illumina HiSeq2000 to produce 100 bp,
 paired-end reads. Reads were quality-assessed using FastQC and quality
 trimmed using Trimmomatic and Cutadapt (to remove adaptor sequences).
 Rcorrector and Jellyfish were used to error-correct reads. Kraken was used
 to remove bacterial, archaeal, and viral contamination. The remaining
 reads (&gt;60 bp) were normalized and assembled using Trinity v2.4.0.
 Assembled contigs were again run through Kraken and analyzed with
 Transdecoder to identify open-reading frames (ORFs) that were at least 100
 amino acids long and to predict likely coding regions. This assembly only
 contains isoforms with the longest ORF per trinity gene. CD-HIT was then
 used to further educe redundancy of the transcripts (similarity threshold
 of 0.95). The assembly was then annotated using dammit.Paramuricea_biscaya_assembly.fastaParamuricea_biscaya_assembly_annotations_dammit