cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hmgqnk9fd
title: Data from: Foraging zebra finches (Taeniopygia guttata) are public information users rather than conformists

description: Social learning enables adaptive information acquisition provided that it
 is not random but selective. To understand species typical decision-making
 and to trace the evolutionary origins of social learning, the heuristics
 social learners use need to be identified. Here, we experimentally tested
 the nature of majority influence in the zebra finch. Subjects
 simultaneously observed two demonstrator groups differing in relative and
 absolute numbers (ratios 1:2 / 2:4 / 3:3 / 1:5) foraging from two novel
 food sources (black and white feeders). We find that demonstrator groups
 influenced observers’ feeder choices (social learning), but that zebra
 finches did not copy the majority of individuals. Instead, observers were
 influenced by the pecks of their demonstrators, and in an anti-conformist
 fashion. These results indicate that zebra finches are not conformist, but
 are public information users.
description: Experimental data. Scored from video.
DOI: 10.5061/dryad.mpg4f4qxd
title: Dietary analysis of the House Swift, Apus nipalensis, in Hong Kong using prey DNA in faecal samples

description: Background
             To understand the dietary composition of the highly aerial swift (Apodidae), ecologists conventionally depend on the morphological identification of prey items from food boluses or stomach contents, but these techniques are often invasive, require expertise in identification, and often cannot produce accurate identifications at the species level. Methods             In this study, DNA barcoding was used to analyse the dietary composition of House Swifts (Apus nipalensis) in Hong Kong. Faecal samples from five different colonial nest sites were collected between 2019 and 2020. We used universal primers to amplify a region of the cytochrome c oxidase gene from prey DNA in the faecal samples for identification purposes. Results             Ten different orders and 44 families from three different classes of Arthropoda were identified in the faecal samples collected. Hymenoptera, Hemiptera and Diptera were the most prevalent groups of prey found in the samples. Differences in the dietary composition of House Swifts during the breeding (April to September) and non-breeding (October to March) seasons were also found. Hymenoptera, particularly ants (Formicidae), were predominant in the diet during the breeding season, whereas Diptera and Hemiptera were predominant during the non-breeding season. Conclusion             The prey groups identified in this study were similar to those identified in a previous study of the diet of House Swifts, which suggests a possible role of House Swifts in reducing the numbers of local insect pests. This study demonstrates the usefulness of applying molecular tools for the dietary analysis of aerial feeders. Conserving local forested areas may be crucial for the maintenance of the House Swift population.
DOI: 10.5061/dryad.3xsj3txf8
title: Bird species in the diet of the birdlike noctule bat, Nyctalus aviator, in Japan.

description: We investigate the birds in the diet of the birdlike noctule (Nyctalus
 aviator) through DNA amplification from feather remains found in fecal
 pellets. Our goal was to confirm that N. aviator preys on nocturnally
 migratory species, as does its European relative N. lasiopterus, and to
 gain insights into this hunting strategy (e.g. on the wing vs. from
 cavity-nest). The diversity and the characteristics of the birds found in
 the feces remains indicate that in Japan N. aviator employs a similar
 hunting strategy on songbirds as N. lasiopterus in Iberia.  Both
 noctules are primarily generalist insectivores that prey on 5-25 g body
 mass songbirds seasonally during their migration and probably hunt them at
 high altitude. Accordingly, predation on birds seems to be a strategy that
 appears in distant points across the Palearctic and is not the result of
 local specialization. We hypothesize that the bird hunting behavior
 appeared during evolution as a trophic jump from a pre-existing hunting
 behavior on the many insects that carry out seasonal nocturnal migrations
 in temperate zones at high-altitude.
DOI: 10.5061/dryad.np5hqbzr8
title: Back into the past: Resurveying random plots to track community changes in Italian coastal dunes

description: This dataset includes two excel sheets. The first contains
 vegetation data ("species_data", a matrix of 668 plots x 213
 species) and the second contains plant functional traits data
 ("traits_data") that were used to evaluate temporal changes in
 taxonomic and functional diversity of Mediterranean coastal dune habitats.
 As to the first sheet ("species_data"): vegetation data were
 collected at two points in time (Time 0, hereafter T0:
 2002-2007, and Time 1, herafter T1: 2017-2018) in 334
 randomly-sampled, georeferenced, standardized (4 m2) plots. Historical
 data used for the resurveying study were extracted from RanVegDunes
 (Sperandii et al. 2017). Details on the resurveying protocol can be found
 in Sperandii et al. (2019), but in short: resampling activities
 took place during the same months in which the original sampling
 was done, and plot positions were relocated using a GPS unit on
 which historical geographic coordinates were stored. Plots are
 located in coastal dune sites along the Tyrrhenian and Adriatic
 coasts of Central Italy, and belong to herbaceous communities classified
 into the following EU Habitats (sensu Annex I 92/43/EEC): upper
 beach (Habitat 1210), embryo dunes (Habitat 2110), shifting dunes (Habitat
 2120), fixed dunes (Habitat 2210), and dune grasslands (Habitat
 2230). A subset of plots could not be classified into an EU
 Habitat because they were highly disturbed or invaded by alien species
 (“NC-plots”). The matrix includes cover data, expressed as percentage (%)
 cover.  As to the second sheet ("traits_data"):
 this sheet includes data on 3 plant functional traits, two of
 them quantitative (plant height, specific leaf area - SLA) and
 one qualitative (plant lifespan). Data for the quantitative
 traits represent species-level average trait values and
 were extracted from “TraitDunes”, a database registered on the
 global platform TRY (Kattge et al., 2020). Functional trait data were
 collected in the same sites covered by the resurveying study. Functional
 trait data were originally measured on the most abundant species, and are
 available for a varying number of species depending on the trait.
 References: Kattge, J., Bönisch, G., Díaz, S., Lavorel, S., Prentice, I.
 C., Leadley, P., ... & Wirth, C. (2020). TRY plant trait
 database–enhanced coverage and open access. Global Change
 Biology. Sperandii, M.G., Prisco, I., Stanisci, A., & Acosta,
 A.T.R (2017). RanVegDunes-A random plot database of Italian
 coastal dunes. Phytocoenologia, 47(2), 231-232.
 Sperandii, M.G., Bazzichetto, M., Gatti, F., & Acosta, A.T.R.
 (2019). Back into the past: Resurveying random plots to track
 community changes in Italian coastal dunes. Ecological
 Indicators, 96, 572-578.
DOI: 10.5061/dryad.m0cfxpp23
title: Data from: Group-specific expressions of co-feeding tolerance in bonobos and chimpanzees preclude dichotomous species generalizations

description: The human species exhibits a remarkable level of social tolerance which
 has propelled a plethora of behavioural expressions pivotal to our
 biological success. To date, the evolutionary origins of humans’
 “ultra-sociality” remain unclear, despite a substantial research focus on
 our closest living evolutionary relatives, the great apes. Bonobos are
 typically portrayed as more socially tolerant than chimpanzees and
 consequentially (sometimes) presented as a better model to study the
 evolutionary roots of human sociality. Yet, the current evidence
 supporting such a species-level categorization is equivocal. Here, we used
 validated group-level co-feeding tasks to test 16
 independent Pan groups living in zoo (n=9) and sanctuary
 (n=7) settings, representing 225 individuals. We found that the
 expressions of social tolerance substantially overlapped between species,
 thus precluding categorical inference at the species level. Instead,
 marked differences were observed among groups, with some bonobo groups
 exhibiting higher social tolerance than chimpanzee groups, and vice versa.
 Interestingly, substantial intergroup variation was found within species
 living in the same environment, which attests to Pan’s
 behavioural flexibility. We conclude that the pervasive dichotomy between
 the tolerant bonobo and the belligerent chimpanzee requires quantitative
 nuance, and that accurate phylogenetic tracing of (human) social behaviour
 necessitates estimations of intraspecific intergroup variation.
DOI: 10.5061/dryad.51c59zw6m
title: Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)

description: The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises
 exclusively parasitoid and kleptoparasitic species, many of which feature
 a stunning iridescent coloration and phenotypic adaptations to their
 parasitic life style. Previous attempts to infer phylogenetic
 relationships among the family’s major lineages (subfamilies, tribes,
 genera) based on Sanger sequence data were insufficient to statistically
 resolve the monophyly and the phylogenetic position of the subfamily
 Amiseginae and the phylogenetic relationships among the tribes
 Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we
 present a phylogeny inferred from nucleotide sequence data of 492 nuclear
 single-copy genes (230,915 aligned amino acid sites) from 94 species of
 Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae,
 Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target
 enrichment data. We find support for Amiseginae being more closely related
 to Cleptinae than to Chrysidinae. Furthermore, we find strong support for
 Allocoeliini being the sister lineage of all remaining Chrysidinae, while
 Elampini represent the sister lineage of Chrysidini and Parnopini. Our
 study corroborates results from a recent phylogenomic investigation which
 revealed Chrysidoidea as likely paraphyletic
DOI: 10.15468/dl.d6y3mk
title: Occurrence Download

description: A dataset containing 404 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cladrastis kentukea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 404 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002634-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b8gtht7b7
title: The oldest Devonian circumpolar ray-finned fish?

description: Actinopterygians (ray-finned fishes) are the most diverse group of living
 fishes, but have a sparse early fossil record restricted to low
 palaeolatitudes. Here we report a new actinopterygian from the Paraná
 Basin of Brazil, an area that occupied a circumpolar position in the
 Palaeozoic. Available geological evidence supports a Middle Devonian or
 older age for this taxon, which shares features of the mandibular
 symphysis with the latest Devonian Tegeolepis. A phylogenetic analysis
 resolves these two as sister taxa. This new record expands the
 palaeogeographic distribution of Devonian ray-fins, and suggests that gaps
 in the early actinopterygian fossil record might be filled by exploring
 poorly sampled high-latitude localities within the Malvinokaffric Realm.
description: The specimen (Museu de Ciências da Terra, Rio de Janeiro, Brazil,
 MCT890-P) was scanned with a GE Phoenix v|tome|x m scanner in the Museu de
 Zoologia da Universidade de São Paulo. We also scanned a dentary of
 <i>Tegeolepis clarki</i> (Cleveland Museum of Natural History,
 Cleveland, USA, CMNH 8124) with a Nikon XT H 225 ST scanner in the
 Department of Earth and Environmental Sciences, University of
 Michigan.
description: Information on data content and usage is available on the
 "README.txt" file.
DOI: 10.15468/dl.6q86yp
title: Occurrence Download

description: A dataset containing 541 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dypsis madagascariensis"
 ]
}

 The dataset includes 541 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002635-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.79cnp5ht1
title: Data from: Functional diversity of decomposers modulates litter decomposition affected by plant invasion along a climate gradient

description: 1. Litter decomposition is fundamental to carbon (C) and nutrient cycling
 in ecosystems, which could be altered by plant invasion. The impacts of
 plant invasion on litter decomposition are generally predicted by traits
 difference between leaf litters of invasive and non-invasive species.
 However, plant invasion not only changes litter composition, but might
 also increase the activity or change the functional diversity of
 decomposers to alter litter decomposition, which is barely studied, and
 the effect could be different under varied climate conditions. 2. We
 studied decomposition of litters from non-invasive and invasive native
 plants, as affected by litter treatments (in a mixture or alone) and
 decomposer organisms of different functional groups (by controlling the
 mesh size of litterbags), in sites with or without an invasive woody
 grass, Moso bamboo (Phyllostachys edulis), at seven locations across a
 climate gradient. 3. We show that greater decomposer functional diversity,
 particularly the presence of macrofauna, accelerated the cycling of litter
 C and nitrogen (N), increased the climatic sensitivities of decomposition
 rates, but decreased the N use efficiency of decomposers (represented by
 litter C to N loss ratio). Litter decomposed in mixtures decomposed faster
 (by 9.5%) and had more N loss (by 28.9%) than that of in monoculture,
 regardless of the functional diversity of decomposers. In contrast, the
 invasion of Moso bamboo slowed decomposition and decreased N use
 efficiency; this negative effect could be reversed when macrofauna was
 excluded from the decomposition process, which challenges the nutrient
 facilitation hypothesis. Bamboo invasion depressed the climatic
 sensitivity of decomposer functional groups when macrofauna was present
 but not when macrofauna was excluded. 4. Synthesis. We found that the
 functional diversity of decomposer organisms modulates and largely
 determines litter decomposition affected by a woody grass invasion along a
 climate gradient. These results suggest that, under current and future
 climate, including the changes in decomposer functional groups,
 particularly macrofauna, and their interaction with litter traits, would
 provide a mechanistic and more reliable prediction on ecosystem functions
 altered by invaders than a functional trait-based framework.
description: Litter decay rates (<em>k</em>), N loss (% of
 initial), C loss (% of initial) of Moso bamboo (<i>Phyllostachys
 edulis</i>) and other species that incubated as single litter
 species and mixtures in different forest types (bamboo forest, non-invaded
 forest, and bamboo invaded forest) at seven locations along climatic
 gradient.
DOI: 10.5061/dryad.gtht76hk4
title: TweetyNet results

description: This dataset accompanies the eLife publication "Automated annotation
 of birdsong with a neural network that segments spectrograms". In the
 article, we describe and benchmark a neural network architecture,
 TweetyNet, that automates the annotation of birdsong as we describe in the
 text. Here we provide checkpoint files that contain the weights of trained
 TweetyNet models. The checkpoints we provide correspond to the models that
 obtained the lowest error rates on the benchmark datasets used (as
 reported in the Results section titled "TweetyNet annotates with low
 error rates across individuals and species"). We share these
 checkpoints to enable other researchers to replicate our key result, and
 to allow users of our software to leverage them, for example to improve
 performance on their data by adapting pre-trained models with transfer
 learning methods.  
description: Checkpoint files were generated using the `vak` library
 (https://vak.readthedocs.io/en/latest/), running it with configuration
 files that are part of the code repository associated with the TweetyNet
 manuscript (https://github.com/yardencsGitHub/tweetynet). Those "config files" are in the directory "article/data/configs" and can be run on the appropriate datasets (as described in the paper). The "source data" files used to generate the figures were created by running scripts on the final results of running the `vak` library. Those source data files and scripts are in the code repository as well. For further detail, please see the methods section in https://elifesciences.org/articles/63853
description: Please see README at https://github.com/yardencsGitHub/tweetynet/blob/master/article/README.md that explains how to install the software. To replicate the key result as described in the section of the article "TweetyNet annotates with low error rates across individuals and species", please follow the set-up instructions in that README, and then run this script: https://github.com/yardencsGitHub/tweetynet/blob/master/article/src/scripts/replicate-key-result/runall.sh For guidance on how to adapt pre-trained models to new datasets, please see the `vak` documentation: https://vak.readthedocs.io/en/latest/
DOI: 10.5061/dryad.905qfttjd
title: Inhibition of firefly luciferase activity by a HIF prolyl hydroxylase inhibitor

description: The three hypoxia-inducible factor (HIF) prolyl-4-hydroxylase domain (PHD)
 1–3 enzymes confer oxygen sen-sitivity to the HIF pathway and are novel
 therapeutic targets for treatment of renal anemia. Inhibition of thePHDs
 may further be beneficial in other hypoxia-associated diseases, including
 ischemia and chronic in-flammation. Several pharmacologic PHD inhibitors
 (PHIs) are available, but our understanding of their selectivity and its
 chemical basis is limited.We here report that the PHI JNJ-42041935
 (JNJ-1935) is structurally similar to the firefly luciferase substrate
 D-luciferin. Our results demonstrate that JNJ-1935 is a novel inhibitor of
 firefly luciferase enzymatic activity. In contrast, the PHIs FG-4592
 (roxadustat) and FG-2216 (ICA,BIQ,IOX3,YM311) did not affect firefly
 luciferase. The JNJ-1935 mode of inhibition is competitive with a Ki of
 1.36 μM. D-luciferin did not inhibit the PHDs, despite its structural
 similarity to JNJ-1935. This study provides insights into a previously
 unknown JNJ-1935 off-target effect as well as into the chemical
 requirements for firefly luciferase and PHD inhibitors and may inform the
 development of novel compounds targeting these enzymes.
DOI: 10.5061/dryad.f4qrfj6tw
title: Large mammalian herbivores contribute to conspecific negative density dependence in a temperate forest

description: 1. The Janzen-Connell Hypothesis (JCH) predicts that density-responsive
 and host-specific natural enemies limit the population sizes of abundant
 species. Importantly, these interactions help to maintain local community
 diversity through time. While ample evidence exists for the demographic
 predictions of the JCH, it remains unclear which natural enemies drive
 these dynamics across different plant communities. 2. While large
 mammalian herbivores are often assumed to lack the specialized diet needed
 to drive Janzen-Connell effects, they do show a degree of host-preference
 that could drive density-dependent plant demography. However, the
 potential role of large mammalian herbivores in Janzen-Connell
 interactions has only rarely been investigated. 3. Using 204 seedling
 transects (1 x 10 m) at 51 sites across a 900-hectare forested reserve in
 southwestern Pennsylvania (USA), we examined the role that large mammals
 play in driving conspecific negative density dependence (CNDD) in
 temperate tree seedlings. Individual fences were erected around half of
 the transects (N=102) to exclude large mammals, and were paired with
 adjacent unfenced transects. Within transects, a total of ~15,000
 individual seedlings were monitored over three growing seasons. 4.
 Demographic neighborhood models were constructed to examine the influence
 of neighborhood composition and density on seedling survival and growth.
 An interaction term between conspecific neighbor density and fencing
 treatment was included to test the hypothesis that large herbivores cause
 CNDD. 5. We found that seedling survival was influenced by both
 conspecific neighbor density and fencing. CNDD was strongest when large
 mammals were allowed access to seedlings, and these results were driven by
 two abundant taxa (Prunus serotina and Fraxinus spp). Despite evidence
 that large mammals mediate CNDD, we found no effect of fencing on rarified
 species richness or evenness in seedling transects during the study. 6.
 Synthesis: Debate regarding the role of large herbivores in fostering the
 diversity and stability of forest communities continues. Our results
 indicate that large mammalian herbivores can cause CNDD in some temperate
 tree species, but whether they help to promote community diversity over
 time remains unclear. Further research is needed to assess the role of
 large mammalian herbivores in driving conspecific negative density
 dependence in plant communities.
description: See ReadMe file for list of column descriptions.