cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6j700
title: Data from: Long-term effects of early nutrition and environmental matching on developmental and personality traits in zebra finches

description: Developmental plasticity is a key feature of many organisms and
 individuals can benefit from early programming to optimize their
 phenotypes for the expected environmental conditions. However,
 environmental conditions may sometimes change unexpectedly. Mismatches
 between early and adult life, for example, can have important
 repercussions for adult phenotypes, potentially leading to better
 performance under matched than mismatched conditions as predicted by the
 predictive adaptive response hypothesis. We conducted a long-term
 experimental manipulation of dietary conditions in a population of zebra
 finches, Taeniopygia guttata. Broods were exposed to two early nutritional
 treatments until independence and we used a split-brood design to
 independently manipulate nutritional conditions after independence to
 create matched and mismatched nutritional environments in later life.
 Developmental trajectories of all individuals were followed for more than
 5 years and we scored behavioural responses in trials in a special
 environment and while interacting with a special object three times during
 adult life. Overall, we found no evidence for early programming affecting
 morphology. Tarsus and wing length were exclusively influenced by the
 early nutrition. Body weight showed lasting effects of the early treatment
 and independent effects of nutritional condition during adulthood, but no
 effects of environmental matching or mismatching. Special-object trials
 showed effects of the adult nutritional treatment while environmental
 matching affected hopping activity in special environments. These
 behavioural responses showed substantial long-term individual stability
 over a 3-month period and were only marginally smaller when measured over
 a period of more than 4 years. Interestingly, survival of individuals from
 low-quality early nutritional condition was higher compared with
 high-quality early condition individuals, which became evident only after
 years of survival monitoring. Beyond the nutritional treatment itself, we
 found sizable brood identity effects that slowly but steadily declined
 with age, indicating a significant but decaying effect of natural
 variation in parental provisioning on adult phenotypes.
description: Morphological data and
 survivalRaw data of the survival
 and morphological traits (body weight, tarsus length, wing length) from
 day 0 to day 2000.Krause Krüger
 Schielzeth_Morph.txtBehavioural
 dataRaw data of the
 behavioural trials (special environment and special object) conducted
 thrice during the life, at the age of 100, 200 and 1600
 days.Krause
 Krüger Schielzeth_Behav.txt
DOI: 10.5061/dryad.38537
title: Data from: Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change

description: While the history of taxonomic diversification in open ocean lineages of
 ray-finned fish and elasmobranchs is increasingly known, the evolution of
 their roles within the open ocean ecosystem remains poorly understood. To
 assess the relative importance of these groups through time, we measured
 the accumulation rate of microfossil fish teeth and elasmobranch dermal
 denticles (ichthyoliths) in deep-sea sediment cores from the North and
 South Pacific gyres over the past 85 million years (Myr). We find three
 distinct and stable open ocean ecosystem structures, each defined by the
 relative and absolute abundance of elasmobranch and ray-finned fish
 remains. The Cretaceous Ocean (pre-66 Ma) was characterized by abundant
 elasmobranch denticles, but low abundances of fish teeth. The Palaeogene
 Ocean (66–20 Ma), initiated by the Cretaceous/Palaeogene mass extinction,
 had nearly four times the abundance of fish teeth compared with
 elasmobranch denticles. This Palaeogene Ocean structure remained stable
 during the Eocene greenhouse (50 Ma) and the Eocene–Oligocene glaciation
 (34 Ma), despite large changes in the overall accumulation of both groups
 during those intervals, suggesting that climate change is not a primary
 driver of ecosystem structure. Dermal denticles virtually disappeared from
 open ocean ichthyolith assemblages approximately 20 Ma, while fish tooth
 accumulation increased dramatically in variability, marking the beginning
 of the Modern Ocean. Together, these results suggest that open ocean fish
 community structure is stable on long timescales, independent of total
 production and climate change. The timing of the abrupt transitions
 between these states suggests that the transitions may be due to
 interactions with other, non-preserved pelagic consumer groups.
description: Ichthyolith Counts for
 DSDP Site 596 and ODP Site 886IODP Sample identifiers,
 downcore depth, age, ichthyolith counts and ichthyolith accumulation rates
 for DSDP Site 596 and ODP Site 886.Sibert_etal_Datasets.xlsx
DOI: 10.5061/dryad.r61r8
title: Data from: Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ Lymphocyte counts greater than 350 cells/mm3: a phase II, multi-centre, double-blind, randomized, placebo-controlled trial

description: Background: Novel tuberculosis vaccines should be safe, immunogenic, and
 effective in various population groups, including HIV-infected
 individuals. In this phase II multi-centre, double-blind,
 placebo-controlled trial, the safety and immunogenicity of the novel
 H1/IC31 vaccine, a fusion protein of Ag85B-ESAT-6 (H1) formulated with the
 adjuvant IC31, was evaluated in HIV-infected adults. Methods: HIV-infected
 adults with CD4+ T cell counts &gt;350/mm3 and without evidence of
 active tuberculosis were enrolled and followed until day 182. H1/IC31
 vaccine or placebo was randomly allocated in a 5:1 ratio. The vaccine was
 administered intramuscularly at day 0 and 56. Safety assessment was based
 on medical history, clinical examinations, and blood and urine testing.
 Immunogenicity was determined by a short-term whole blood intracellular
 cytokine staining assay. Results: 47 of the 48 randomised participants
 completed both vaccinations. In total, 459 mild or moderate and 2 severe
 adverse events were reported. There were three serious adverse events in
 two vaccinees classified as not related to the investigational product.
 Local injection site reactions were more common in H1/IC31 versus placebo
 recipients (65.0% vs. 12.5%, p = 0.015). Solicited systemic and
 unsolicited adverse events were similar by study arm. The baseline CD4+ T
 cell count and HIV viral load were similar by study arm and remained
 constant over time. The H1/IC31 vaccine induced a persistent Th1-immune
 response with predominately TNF-α and IL-2 co-expressing CD4+ T cells, as
 well as polyfunctional IFN-γ, TNF-α and IL-2 expressing CD4+ T cells.
 Conclusion: H1/IC31 was well tolerated and safe in HIV-infected adults
 with a CD4+ Lymphocyte count greater than 350 cells/mm3. The vaccine did
 not have an effect on CD4+ T cell count or HIV-1 viral load. H1/IC31
 induced a specific and durable Th1 immune response.
description: PlosOne H1/IC31 TB
 vaccine studyH1/IC31 TB Subunit
 Vaccine trial in HIV-Infected Adults with CD4+ Lymphocyte Counts Greater
 than 350 cells/mm3plosone_TBvaccine study
 2014.xlsx
DOI: 10.5061/dryad.4q8r207
title: Data from: Maternal and neonatal outcome after vaginal breech delivery at term of children weighing more or less than 3.8 kg: a FRABAT prospective cohort study

description: Introduction: The clinical management of breech presentations at term is
 still a controversially discussed issue among clinicians. Clear predictive
 criteria for planned vaginal breech deliveries are desperately needed to
 prevent adverse fetal and maternal outcomes and to reduce elective
 cesarean section rates. The green-top guideline considers an estimated
 birth weight of 3.8 kg or more an indication to plan a cesarean section
 despite the lack of respective evidence. Objective: To compare maternal
 and neonatal outcome of vaginal intended breech deliveries of births with
 children with a birth weight of 2.5 kg - 3.79 kg and children with a birth
 weight of 3.8 kg and more. Design: Prospective cohort study. Sample: All
 vaginal intended deliveries out of a breech position of newborns weighing
 between 2.5 kg and 4.5 kg at the Obstetrics department at Goethe
 University Hospital Frankfurt from January 2004 until December 2016
 Methods: Neonatal and maternal outcome of a light weight group (LWG)
 (&lt; 3.8 kg) was compared to and a high weight group (HWG) (? 3.8 kg)
 using Pearson's Chi Square test and Fishers exact test. A logistic
 regression analysis was performed to detect an association between
 cesarean section rates, fetal outcome and the birth weight. Results: No
 difference in neonatal morbidity was detected between the HWG (1.8%,
 n=166) and the LWG (2.6%, n=888). Cesarean section rate was significantly
 higher in the HWG with 45.2% in comparison to 28.8% in the LWG with an
 odds ratio of 1.57 (95% CI 1.29-1.91, p&lt;0.0001). In vaginal
 deliveries, a high birth weight was not associated with an increased risk
 of maternal birth injuries (LWG in vaginal deliveries: 74.3%, HWG in
 vaginal deliveries: 73.6%; p=0.887; OR=1.9 (95% CI 0.9 - 1.1)) Conclusion:
 A fetal weight above 3.79 kg does not predict increased maternal or infant
 morbidity after delivery from breech presentation at term. Neither the
 literature nor our analyses document evidence for threshold of estimated
 birth weight that is associated with maternal and/or infant morbidity.
 However, patients should be informed about an increased likelihood of
 cesarean sections during labor when attempting vaginal birth from breech
 position at term in order to reach an informed shared decision concerning
 the birth strategy. Further investigations in multi center settings are
 needed to advance international guidelines on vaginal breech deliveries in
 the context of estimated birth weight and its impact on perinatal outcome.
description: Dataset_Breech_FRABAT
DOI: 10.5061/dryad.80df776
title: Data from: A small yet occasional meal: predatory drill holes in Paleocene ostracods from Argentina and methods to infer predation intensity

description: Ostracods are common yet understudied prey in the fossil record. We
 document drill holes in Paleocene (Danian) ostracods from central
 Argentina using 9025 specimens representing 66 species. While the
 assemblage-level drilling percentage is only 2.3%, considerable variation
 exists within species (0.3–25%), suggesting prey preference by the
 drillers. This preference is not determined by abundance because no
 significant correlation is found between species abundance and drilling
 percentages. Seven methods were used, some of which are new, to quantify
 drilling percentages for the abundant and commonly drilled Togoina
 argentinensis. The obtained range from 9.9 to 14.6% suggests that drilling
 percentages are fairly insensitive to the method used, implying that
 comparisons across studies appear possible. Using this knowledge, the
 Cretaceous-Paleogene mass extinction had limited effect on drilling
 intensity in ostracod prey. The cylindrical (Oichnus simplex) and
 parabolic (O. paraboloides) drill holes from Argentina may have been
 primarily caused by muricid and naticid gastropods. Two oval drill holes
 (O. ovalis) are morphologically similar to octopod drill holes, but their
 small size, the fact that extant octopods are unknown to drill ostracods
 and the absence of such holes in co-occurring gastropods preclude
 ascription to a predator. Drill holes are located preferentially in the
 median and dorsal regions, where most soft tissue including the adductor
 muscle is located. Drilled specimens are statistically taller than
 non-drilled specimens for T. argentinensis and larger predators selected
 larger ostracods. The drilling percentage is significantly higher in
 ornamented ostracods, suggesting that ornamentation is not functional
 against drilling predators here.
description: Data of the drill holes
 and ostracods drilled from the Danian of ArgentinaData of the drill holes
 and ostracods drilled from the Danian (Roca and Jagüel formations) of
 Argentina.Supplementary information
 tableS1Villegas-Martínetal.xlsxValve size measurements
 of drilled and not drilled on Togoina argentinensis from the Danian of
 Argentina.The valve size
 measurements on Togoina argentinensis (drilled and not drilled specimens)
 from the Danian (Roca and Jagüel formations) of Argentina and the type of
 valve found are indicated.Supplementary information table
 S2Villegas-Martínetal.xlsxSpecimen number,
 relative abundance, and drilled and not drilled ostracods from the Danian
 of ArgentinaThe dataset contains the
 specimen number, relative abundance, and drilled and not drilled ostracod
 species for the Roca and Jagüel formations from the Danian of
 Argentina.Supplementary information
 tableS3Villegas-Martinetal.xls
DOI: 10.5061/dryad.55n17h8
title: Data from: Ultraviolet radiation exposure time and intensity modulate tomato resistance against herbivory through activation of the jasmonic acid signaling

description: Ultraviolet (UV) radiation can modulate plant defenses against herbivorous
 arthropods. We investigated how different UV exposure times and irradiance
 intensities affected tomato (Solanum lycopersicum) resistance to thrips
 (Frankliniella occidentalis) by assessing UV effects on thrips-associated
 damage and host-selection, selected metabolite and phytohormone contents,
 expression of defense-related genes, and trichome density and chemistry,
 the latter having dual roles in defense and UV protection. Short UV daily
 exposure times increased thrips resistance in the cultivar ‘Moneymaker’
 but this could not be explained by changes in the contents of selected
 leaf polyphenols or terpenes, nor by trichome-associated defenses. UV
 irradiance intensity also affected resistance to thrips. Further analyses
 using the tomato mutants def-1, impaired in jasmonic acid (JA)
 biosynthesis, od-2, defective in the production of functional type-VI
 trichomes, and their wild-type, ‘Castlemart’, showed that UV enhanced
 thrips resistance in Moneymaker and od-2, but not in def-1 and Castlemart.
 UV increased salicylic acid (SA) and JA-isoleucine concentrations, and
 increased expression of SA- and JA-associated genes in Moneymaker, while
 inducing expression of JA-defensive genes in od-2. Our results demonstrate
 that UV-mediated enhancement of tomato resistance to thrips is probably
 associated with the activation of JA-associated signaling, but not with
 plant secondary metabolism or trichome-related traits.
description: Escobar-Bravo et al.
 JXB
DOI: 10.5061/dryad.8714
title: Data from: Strong male/male competition allows for nonchoosy females: high levels of polygynandry in a territorial frog with paternal care

description: Our knowledge about genetic mating systems and the underlying causes for
 and consequences of variation in reproductive success has substantially
 improved in recent years. When linked to longitudinal population studies,
 cross-generational pedigrees across wild populations can help answer a
 wide suite of questions in ecology and evolutionary biology. We used
 microsatellite markers and exhaustive sampling of two successive adult
 generations to obtain population-wide estimates of individual reproductive
 output of males and females in a natural population of the Neotropical
 frog Allobates femoralis (Aromobatidae), a pan-Amazonian species that
 features prolonged iteroparous breeding, male territoriality, and male
 parental care. Parentage analysis revealed a polygynandrous mating system
 in which high proportions of males (35.5%) and females (56.0%) produced
 progeny that survived until adulthood. Despite contrasting reproductive
 strategies, successfully reproducing males and females had similar numbers
 of mating partners that sired the adult progeny (both sexes: median 2;
 range 1–6); the numbers of their offspring that reached adulthood were
 also similar (both sexes: median 2; range 1–8). Measures of reproductive
 skew indicate selection on males only for their opportunity to breed.
 Reproductive success was significantly higher in territorial than
 non-territorial males, but unrelated to territory size in males or to body
 size in both sexes. We hypothesise that female polyandry in this species
 has evolved due to enhanced offspring survival when paternal care is
 allocated to multiple partners.
description: descriptive statistics
 of microsatellite locifull list of descriptive
 statistics for the seven microsatellite loci
DOI: 10.5061/dryad.0p3j8
title: Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs

description: Microsatellites, also called simple sequence repeats (SSRs) are markers of
 choice to estimate relevant parameters for conservation genetics, such as
 migration rates, effective population size and kinship.
 Cross-amplification of SSRs is the simplest way to obtain sets of markers
 and highly conserved SSRs have recently been developed from Expressed
 Sequence Tags (EST) to improve SRR cross-species utility. As EST-SSRs are
 located in coding regions, the higher stability of their flanking regions
 reduces the frequency of null alleles and improves cross-species
 amplification. However, EST-SSRs have generally less allelic variability
 than genomic SSRs, potentially leading to differences in estimates of
 population genetic parameters such as genetic differentiation. To assess
 the potential of EST-SSRs in studies of within-species genetic diversity,
 we compared the relative performance of EST- and genomic SSRs following a
 multi-species approach on passerine birds. We tested whether patterns and
 levels of genetic diversity within- and between-populations assessed from
 EST- and from genomic SSRs are congruent and we investigated how the
 relative efficiency of EST- and genomic SSRs is influenced by levels of
 differentiation. EST- and genomic SSRs ensured comparable inferences of
 population genetic structure in cases of strong genetic differentiation,
 and genomic SSRs performed slightly better than EST-SSRs when
 differentiation is moderate. However and interestingly, EST-SSRs had a
 higher power to detect weak genetic structure compared to genomic SSRs.
 Our study attests that EST-SRRs may be valuable molecular markers for
 conservation genetic studies in taxa such as birds, where the development
 of genomic SSRs is impeded by their low frequency.
description: Microsatellite
 dataEST- and genomic SSR
 datasetsKhimoun et
 al_MolEcolResources_Microsatellite
 dataset.xlsx
DOI: 10.5061/dryad.6h722
title: Data from: Craniodental indicators of prey size preference in the Felidae

description: In the present study, we used linear morphometrics of the crania, mandible
 and dentition to explore the association between craniodental shape and
 prey size among 35 species of living felids. To accomplish this, felids
 were divided into three prey-size groups: (1) large prey specialists; (2)
 small prey specialists; and (3) mixed prey feeders. From these linear
 measurements, large prey specialist felids can be distinguished from small
 and mixed prey feeders by their relatively robust canines and incisors and
 relatively wide muzzles. These cranial characters are advantageous when
 dispatching large prey, due to the stranglehold that cats employ during
 this activity. Robust canines resist the bending and torsional forces
 applied by struggling prey and a wider muzzle helps to stabilize grip and
 distribute bite forces more evenly during the killing bite. Small prey
 specialists had smaller canines, narrower muzzles and slightly longer jaws
 for a speed advantage when catching small, quick prey. Mixed prey feeders
 were intermediate between large and small prey specialists, indicating
 they are adapted to killing both sizes of prey. Given the success of this
 ecomorphological analysis of living felids that specialize on different
 prey sizes, we look forward to applying this same approach to extinct
 species.
description: Felidae Cranial
 dataCranial and dental data
 from 35 species of wild felids.
DOI: 10.5061/dryad.h44q0
title: Data from: Testing for parallel allochronic isolation in lake-stream stickleback

description: The evolution of reproductive isolation (RI) is a critical step shaping
 progress toward speciation. In the context of ecological speciation, a
 critical question is the extent to which specific reproductive barriers
 important to RI evolve rapidly and predictably in response to
 environmental differences. Only reproductive barriers with these
 properties (importance, rapidity, predictability) will drive the
 diversification of species that are cohesively structured by environment
 type. One candidate barrier that might exhibit such properties is
 allochrony, whereby populations breed at different times. We studied six
 independent lake-stream population pairs of threespine stickleback
 (Gasterosteus aculeatus Linnaeus, 1758) that are known from genetic
 studies to show RI. However, the specific reproductive barriers driving
 this RI have proven elusive, leading to a “conundrum of missing
 reproductive isolation.” We here show that breeding times differ among
 some of the populations, but not in a consistent manner between lakes and
 streams. Moreover, the timing differences between lake and stream
 populations within each pair could account for only a small proportion of
 total RI measured with neutral genetic markers. Allochrony cannot solve
 the conundrum of missing reproductive isolation in lake-stream
 stickleback.
description: Fish sex and maturity
 scoresFirst column contains
 the ID of the collection, which indicates the location of the collection.
 Second column is a unique ID for each fish. Third column is the sex of the
 fish; male = M, female = F, unknown = U. Fourth column is the maturity
 score if the fish is female; 1=gravid but eggs not visible or running,
 2=eggs visible but not running, 3=eggs running. If fish is male or
 unknown, a zero will be recorded in this column. Fifth column is the
 maturity score if the fish is male; 1=just enough colour to identify as
 male, 2=red colour on throat, mouth, snout, and operculum and/or blue
 colour on eye, posterior flank, and area around the testes, 3=intense and
 extensive red colour on throat, mouth, snout, and operculum and/or blue
 colour on eye, posterior flank, and area around the testes. If fish is
 female or unknown, a zero will be recorded in this
 column.fish_data.csv
DOI: 10.34740/kaggle/dsv/14633561
title: Peer-to-Peer Boliviano (BOB) Exchange Data