cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v8921
title: Data from: Walking on ashes: insect trace fossils from Laetoli indicate poor grass cover associated with early hominin environments

description: More than 4000 insect trace fossils collected in recent years from
 Pliocene deposits at Laetoli in northern Tanzania provide new insights on
 early hominin palaeoenvironments. These trace fossils include:
 Fictovichnus gobiensis, Coprinisphaera murguiai, C. kheprii,
 Coprinisphaera ispp., Quirogaichnus isp., Teisseirei linguatus isp. nov.,
 Celliforma ritchiei isp. nov., C. spirifer, C. germanica, C. cfr. curvata,
 Celliforma ispp., Rosellichnus isp., Vondrichnus planoglobus, Laetolichnus
 kwekai igen. et isp. nov. and Krausichnidae indet. They reveal that at
 least one species of moth, three dung beetles and five other coleopterans,
 nine taxa of solitary bees, and an indeterminate number of taxa of
 termites inhabited the Lower Laetolil environments. The Upper Laetolil
 environments, which have yielded a rich diversity of vertebrate fossils,
 including the early hominin Australopithecus afarensis and its putative
 footprints, supported several taxa of termites, one dung beetle, five
 other coleopterans, and eleven taxa of bees. The Upper Ndolanya
 environments, which have yielded the hominin Paranthropus aethiopicus,
 record four taxa of dung beetles, four other coleopterans, and two taxa of
 bees. The record of larval mortality and lack of intruder activity,
 revealed by the absence of emergence and intruder traces, may be
 associated with the anoxic/hypoxic conditions caused by the instantaneous
 burial of soils under thick volcanic ashes. The record of the Celliforma
 Ichnofacies in the Upper Laetolil environments indicates the dominance of
 shrubland to woodland with limited grass cover. This is supported also by
 the absence of Coprinisphaera, which suggests a scarcity of fresh grasses
 and a low abundance of large mammal grazers.
description: Examined
 materialThis is the list of
 specimens examined for each ichnotaxon.Supporting Information Genise _
 Harrison.docx
DOI: 10.4121/a6d5a40e-0358-47cf-9ec1-335df0e4a3c3
title: Data underlying the publication: An integrated end-to-end deep neural network for automated detection of discarded fish species and their weight estimation.

description: The dataset contains images of the discarded fish on the conveyor belt and annotations. Annotations are prepared in YOLO format, i.e. separate text files, containing fish species label, object bounding box annotation, weight and occlusion level. Annotation per individual fish is written in a separate row of the file.Additionally, we provide weight file (.pt) for the best performing Detection-Weight2 model.
DOI: 10.4121/a6d5a40e-0358-47cf-9ec1-335df0e4a3c3.v3
title: Data underlying the publication: An integrated end-to-end deep neural network for automated detection of discarded fish species and their weight estimation.

description: The dataset contains images of the discarded fish on the conveyor belt and annotations. Annotations are prepared in YOLO format, i.e. separate text files, containing fish species label, object bounding box annotation, weight and occlusion level. Annotation per individual fish is written in a separate row of the file.Additionally, we provide weight file (.pt) for the best performing Detection-Weight2 model.
DOI: 10.5061/dryad.559m9
title: Data from: Six new cryptic species of Xylodonta Becker, 2014 (Notodontidae: Nystaleinae) from Costa Rica

description: The genus Xylodonta Becker (Notodontidae, Nystaleinae) is reviewed for
 Costa Rica based on 1,571 reared and wild-collected specimens. Eleven
 species are recorded, of which six are newly described: Xylodonta
 markvanputteni Chacón, Xylodonta patrickgoodwilliei Chacón, Xylodonta
 scottmilleri Chacón, Xylodonta andrewrusselli Chacón, Xylodonta
 robertodelgadoi Chacón, and Xylodonta billhaberi Chacón. Xylodonta terrena
 (Schaus, 1892) and Xylodonta xylinata (Walker, 1865) are redescribed and
 Xylodonta angustipennis (Schaus, 1911), Xylodonta rufitincta (Dyar, 1913),
 and Xylodonta guarana (Schaus, 1892) are discussed. Adults and genitalia
 are illustrated. Species are described and diagnosed through their
 distinctive COI barcodes, genital morphology and life histories. Xylodonta
 adults and caterpillars, and their foodplants in Área de Conservación
 Guanacaste (ACG) in northwestern Costa Rica, are reviewed. Larvae of four
 species are illustrated.
description: Specimens examined of
 XylodontaAdditional specimen data
 accompanying a review of the genus Xylodonta in Costa
 Rica.Xylodonta SUPPLEMENTARY
 INFORMATION.docx
DOI: 10.5061/dryad.q8rp3
title: Data from: Effect of composition on shape of bird eggs

description: Numerous studies over the past 90 years have described the various bird
 egg shapes in mathematical terms but few studies have considered the
 underlying reasons for such interspecific egg shape variability. This
 study investigated how the size and composition, i.e. proportions of
 shell, yolk and albumen, were associated with egg shape. Geometric
 morphometrics were used to generate principal components, which were
 analysed in relation to taxonomy (i.e. avian order) and degree of neonatal
 developmental maturity, which correlates with egg composition. The
 analysis confirmed previous results that most of the variation in shape is
 associated with degree of elongation (i.e. length divided by breadth) and
 asymmetry (i.e. position of the broadest part of the egg away from the
 mid-point of the egg's length). Egg shape reflected avian order but
 not developmental maturity. The degree of elongation of an egg is related
 to absolute egg mass and the proportion of yolk. By contrast, the degree
 of asymmetry is related to the proportion of shell and the mass of the egg
 relative to female body mass. Although significant, the models explained
 little of the variation in egg shape and so it was concluded that other
 factors, such as pelvis size and shape, could be more important in
 determining egg shape in birds.
description: Deeming JAB
 dataData on female body
 mass, egg and egg component mass plus PC values derived from geometric
 morphometric analysis
DOI: 10.5061/dryad.28hv53f
title: Data from: Successional dynamics of the bee community in a tropical dry forest: insights from taxonomy and functional ecology

description: Despite the recent rapid growth of tropical dry forest succession ecology,
 most studies on this topic have focused on plant community attribute
 recovery, whereas animal community successional dynamics has been largely
 overlooked, and the few existing studies have used taxonomic approaches.
 Here, we analyze the successional changes in the bee community in a
 Mexican tropical dry forest, by integrating taxonomic (species, genus, and
 family diversity) and functional (sociability, nesting strategy, and body
 size) information for bees. Over one year, in a successional
 chronosequence (2–67 years after abandonment) we collected 469 individual
 bees, representing five families, 36 genera and 69 species. Linear
 modeling showed decreases in taxonomic diversity with succession, more
 strongly so for species. Bee species turnover along succession ranged from
 moderate to high, decreasing slightly at intermediate stages. An RLQ
 analysis (ordination method that allows relating environmental variables
 with functional attributes) revealed clear relations between bee
 functional traits and the plant community. RLQ axis 1 was positively
 related to vegetation structural and diversity variables, and to
 eusociality, whilst solitary, parasociality and ground nesting were
 negatively associated with it. Early successional fallows attract mostly
 solitary and parasocial bees; older fallows tend to attract eusocial bees
 with aerial nesting. The continuous taxonomic turnover observed by us and
 the functional analysis suggest that the disappearance of old fallows from
 agricultural landscapes would likely result in significant reductions and
 even local extinctions of particular bee guilds. Considering the low
 viability of preserving large mature tropical dry forest tracts, the
 conservation of older successional stands emerges as a crucial component
 of landscape management.
description: Ramos-Fabiel et al
 DataBaseThe data contained in
 this data base are from nine tropical dry forest secondary plots (30 × 30
 m; 0.09 ha) representing a successional chronosequence, with ages ranging
 between 2 and 67 years after abandonment. The plots are located around the
 village of Nizanda, Oaxaca state, southern Mexico. The format is an Excel
 Book. Page 'SITES' contains the characteristics of these plots,
 including geographical location and elevation. Page 'VEGETATION
 ATTRIBUTES' contains structural and diversity attributes of the
 vegetation at each sampling site. Page 'BEE FUNCTIONAL
 ATTRIBUTES' contains information for bee guild, nesting habit and
 body size for each bee species. Page 'BEE ABUNDANCES' contains
 the numbers of individuals for each bee species at each sampling site.
 Page 'BEE FAMILIES BY PLANT SPECIES' contains the numbers of
 individuals belonging to each of five bee families that were trapped on
 each plant species over the study period.
DOI: 10.15468/dl.44g2jd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Filippovia knipovitchi",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001193-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.3h45m
title: Data from: The male handicap: male-biased mortality explains skewed sex ratios in brown trout embryos

description: Juvenile sex ratios are often assumed to be equal for many species with
 genetic sex determination, but this has rarely been tested in fish embryos
 due to their small size and absence of sex-specific markers. We
 artificially crossed three populations of brown trout and used a recently
 developed genetic marker for sexing the offspring of both pure and hybrid
 crosses. Sex ratios (SR = proportion of males) varied widely one month
 after hatching ranging from 0.15 to 0.90 (mean = 0.39 ± 0.03). Families
 with high survival tended to produce balanced or male-biased sex ratios,
 but SR was significantly female-biased when survival was low, suggesting
 that males sustain higher mortality during development. No difference in
 SR was found between pure and hybrid families, but the existence of sire ×
 dam interactions suggests that genetic incompatibility may play a role in
 determining sex ratios. Our findings have implications for animal breeding
 and conservation because skewed sex ratios will tend to reduce effective
 population size and bias selection estimates.
description: Table S3. Trout sex
 databaseCSV file with parental
 traits and family data on survival and sex ratios
DOI: 10.5061/dryad.46r48
title: Data from: Effect of acute stressor on reproductive behavior differs between urban and rural birds

description: The life-history trade-off between self-maintenance and reproduction
 posits that investment in one function decreases investment in the other.
 Manipulating the costs and benefits of functions involved in a trade-off
 may alter this interaction. Here we ask whether investment in
 self-maintenance during a stress response alters territorial behavior in
 wild Dark-eyed Juncos and whether rural and urban birds, which are known
 to differ in the magnitude of the stress response (greater in rural), also
 differ in the degree to which stress reduces territorial behavior. In
 rural and urban habitats, we measured territorial behavior using song
 playback, followed by either an acute stressor (capture and collection of
 a blood sample) or a nonstressful control situation. The following day, we
 again measured territorial behavior, predicting greater reduction in
 territorial behavior in individuals exposed to the stressor but a lesser
 reduction in territorial behavior in the urban as compared to the rural
 environment. We further assessed individual and population differences in
 response to stressors by measuring flight initiation distance, breath
 rate, and corticosterone levels in the blood. The rural population had a
 higher physiological and behavioral stress response than the urban
 population, and acute capture stress had a lasting (24 h) negative effect
 on territorial behavior, but only in the rural habitat. However,
 individual-level differences in measures of the stress response did not
 explain variation in the impact of stress on territorial behavior. Our
 findings show that stressors can have a negative effect on territorial
 behavior, but that this effect may differ between populations that vary in
 their stress ecology.
description: Stress study and
 hormonesMain data
 setstress
 study and hormones.csvpopulation
 FIDadditional data
 set
DOI: 10.5061/dryad.2r8v4
title: Data from: C:N:P stoichiometry in China's forests: from organs to ecosystems

description: Ecological stoichiometry connects different levels of biology, from the
 gene to the globe, by scaling up elemental ratios (e.g., carbon [C],
 nitrogen [N], and phosphorus [P]). Thus, ecological stoichiometry could be
 a powerful tool for revealing certain physiological processes of plants.
 However, C:N:P stoichiometry remains unclear at the community and
 ecosystem level, despite it being potentially important for primary
 productivity. In this study, we measured the C, N, and P content of
 different plant organs, litter, and soil in 9 natural forest ecosystems
 (cold-temperate to tropical forests along a 3700-km transect in China) to
 explore C:N:P stoichiometry and the main influencing factors. C:N:P
 stoichiometry was evaluated for different components in the forest
 ecosystems (plant community, soil, litter, and ecosystem) and, at the
 community level, for different organs (leaves, branches, trunks, and
 roots) from 803 plant species. The ratios of C:P and N:P decreased with
 increasing latitude, with spatial patterns being primarily regulated by
 climate. Interestingly, the homeostasis of N, P, and N:P was highest in
 leaves, followed by branches, roots, and trunk, supporting the hypothesis
 that more active organs have a higher capacity to maintain relatively
 stable element content and ratios. At the community level, the leaf N:P
 ratio indicated increasing P limitation in forests of lower latitude
 (i.e., more southerly) in China's forests. Our findings demonstrate
 the spatial patterns of C:N:P stoichiometry and the strategies of element
 distribution among different organs in a plant community, providing
 important data on C:N:P to improve the parameterization of future
 ecological models.
description: C:N:P stoichiometry in
 China’s forests: from organs to ecosystemsFE-2016-01083-Data
 Accessibility.xlsx
DOI: 10.5061/dryad.c8v3rv6
title: Data from: Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

description: Recent exploration into the interactions and relationship between hosts
 and their microbiota has revealed a connection between many aspects of the
 host's biology, health and associated micro‐organisms. Whereas
 amplicon sequencing has traditionally been used to characterize the
 microbiome, the increasing number of published population genomics data
 sets offers an underexploited opportunity to study microbial profiles from
 the host shotgun sequencing data. Here, we use sequence data originally
 generated from killer whale Orcinus orca skin biopsies for population
 genomics, to characterize the skin microbiome and investigate how host
 social and geographical factors influence the microbial community
 composition. Having identified 845 microbial taxa from 2.4 million reads
 that did not map to the killer whale reference genome, we found that both
 ecotypic and geographical factors influence community composition of
 killer whale skin microbiomes. Furthermore, we uncovered key taxa that
 drive the microbiome community composition and showed that they are
 embedded in unique networks, one of which is tentatively linked to diatom
 presence and poor skin condition. Community composition differed between
 Antarctic killer whales with and without diatom coverage, suggesting that
 the previously reported episodic migrations of Antarctic killer whales to
 warmer waters associated with skin turnover may control the effects of
 potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our
 work demonstrates the feasibility of microbiome studies from host shotgun
 sequencing data and highlights the importance of metagenomics in
 understanding the relationship between host and microbial ecology.
description: RAW_SPECIES_SUMRead counts per bacterial taxa summed across all individual killer whalesCoverage CheckerThis scripts identifies for each genome if certain regions are covered much higher than the genome-wide average.check_coverage.pyDuplicate read removal scriptThis scripts identifies all reads with identical sequences and only writes the first occurence of a read to the output.remove_duplicates_single_end.py
DOI: 10.5061/dryad.66jd4
title: Data from: Broad-scale trophic shift in the pelagic North Pacific revealed by an oceanic seabird

description: Human-induced ecological change in the open oceans appears to be
 accelerating. Fisheries, climate change and elevated nutrient inputs are
 variously blamed, at least in part, for altering oceanic ecosystems. Yet
 it is challenging to assess the extent of anthropogenic change in the open
 oceans, where historical records of ecological conditions are sparse, and
 the geographical scale is immense. We developed millennial-scale amino
 acid nitrogen isotope records preserved in ancient animal remains to
 understand changes in food web structure and nutrient regimes in the
 oceanic realm of the North Pacific Ocean (NPO). Our millennial-scale
 isotope records of amino acids in bone collagen in a wide-ranging oceanic
 seabird, the Hawaiian petrel (Pterodroma sandwichensis), showed that
 trophic level declined over time. The amino acid records do not support a
 broad-scale increase in nitrogen fixation in the North Pacific subtropical
 gyre, rejecting an earlier interpretation based on bulk and amino acid
 specific δ15N chronologies for Hawaiian deep-sea corals and bulk δ15N
 chronologies for the Hawaiian petrel. Rather, our work suggests that the
 food web structure in the NPO has shifted at a broad geographical scale, a
 phenomenon potentially related to industrial fishing.
description: Ostrom et al Hawaiian
 Petrel amino acid N isotope dataAmino acid specific
 nitrogen isotope data from Hawaiian petrel gelatinOstrom et al Isotope
 Data.csv
DOI: 10.5061/dryad.c5m0r
title: Data from: Synergistic impacts by an invasive amphipod and an invasive fish explain native gammarid extinction

description: Background: Worldwide freshwater ecosystems are increasingly affected by
 invasive alien species. In particular, Ponto-Caspian gobiid fishes and
 amphipods are suspected to have pronounced effects on aquatic food webs.
 However, there is a lack of systematic studies mechanistically testing the
 potential synergistic effects of invasive species on native fauna. In this
 study we investigated the interrelations between the invasive amphipod
 Dikerogammarus villosus and the invasive fish species Neogobius
 melanostomus in their effects on the native amphipod Gammarus pulex. We
 hypothesized selective predation by the fish as a driver for displacement
 of native species resulting in potential extinction of G. pulex. The
 survival of G. pulex in the presence of N. melanostomus in relation to the
 presence of D. villosus and availability of shelter was analyzed in the
 context of behavioural differences between the amphipod species. Results:
 Gammarus pulex had a significantly higher susceptibility to predation by
 N. melanostomus compared to D. villosus in all experiments, suggesting
 preferential predation by this fish on native gammarids. Furthermore, the
 presence of D. villosus significantly increased the vulnerability of G.
 pulex to fish predation. Habitat structure was an important factor for
 swimming activity of amphipods and their mortality, resulting in a
 threefold decrease in amphipods consumed with shelter habitat structures
 provided. Behavioral differences in swimming activity were additionally
 responsible for higher predation rates on G. pulex. Intraguild predation
 could be neglected within short experimental durations. Conclusions: The
 results of this study provide evidence for synergistic effects of the two
 invasive Ponto-Caspian species on the native amphipod as an underlying
 process of species displacements during invasion processes. Prey behaviour
 and monotonous habitat structures additionally contribute to the decline
 of the native gammarid fauna in the upper Danube River and elsewhere.
description: raw-data for Synergistic
 impacts by an invasive amphipod and an invasive fish explain native
 gammarid extinctionExcel file. Data
 collected in laboratory experiments. Tab 1: Mortality data [%] (1=size
 class small, 2=size class big); Tab 2: Predation data [total number]; Tab
 3: Swimming behaviour [number of free swimming gammarids] (T1-T5:
 Replicate tanks).raw-data.xlsx
DOI: 10.5061/dryad.kn58h
title: Data from: Do personality and innovativeness influence competitive ability? An experimental test in the great tit

description: Competitive ability is a major determinant of fitness, yet why individuals
 vary in their ability to compete for resources is often unclear. Rather
 than simply reflecting inherent differences in the ability of individuals
 to reach an assumed optimum behavior quality, empirical evidence suggests
 that competitive ability may also reflect alternative strategies that
 arise because of correlations with other behaviors, such as innovativeness
 and personality. We examined experimentally how two behavioral traits -
 exploration of a novel environment (an index of the reactive-proactive
 personality axis) and performance in a novel lever pulling task (a measure
 of innovativeness) - were related to the outcomes of dyadic contests
 involving wild-caught great tits. Dyads were then allowed to compete
 freely at a feeder before being exposed to a novel string-pulling task.
 Although we found no significant relationship between exploration behavior
 or innovativeness in isolation and competitiveness, individuals that were
 less competitive were more likely to spontaneously perform the
 string-pulling behavior during the dyadic trials, the first direct
 experimental demonstration of competitive exclusion leading to innovation.
 Our results support the hypothesis that innovations provide a means for
 less competitive individuals to access resources in line with the
 “necessity drives innovation hypothesis”, and we discuss the functional
 significance of innovative behaviors in wild populations.
description: Non-experimental
 dataData for calculating
 repeatabilities of exploration behaviour and problem solving performance
 in isolation, as well as stress analyses.O'Shea_et_al_BEHECO_2017_1.csvExperimental DataData for all experimental analysesO'Shea_et_al_BEHECO_2017_2.csv