cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p8cz8w9mx
title: Data from: How to make methodological decisions when inferring social networks

description: Social network analyses allow studying the processes underlying the
 associations between individuals and the consequences of those
 associations. Constructing and analysing social networks can be
 challenging, especially when designing new studies as researchers are
 confronted with decisions about how to collect data and construct
 networks, and the answers are not always straightforward. The current lack
 of guidance on building a social network for a new study system might lead
 researchers to try several different methods, and risk generating false
 results arising from multiple hypotheses testing. Here, we suggest an
 approach for making decisions when starting social network research in a
 new study system that avoids the pitfall of multiple hypotheses testing.
 We argue that best edge definition for a network is a decision that can be
 made using a priori knowledge about the species, and that is independent
 from the hypotheses that the network will ultimately be used to evaluate.
 We illustrate this approach with a study conducted on a colonial
 cooperatively breeding bird, the sociable weaver. We first identified two
 ways of collecting data using different numbers of feeders and three ways
 to define associations among birds. We then evaluated which combination of
 data collection and association definition maximised (i) the assortment of
 individuals into previously known ‘breeding groups’ (birds that contribute
 towards the same nest and maintain cohesion when foraging), and (ii)
 socially differentiated relationships (more strong and weak relationships
 than expected by chance). This evaluation of different methods based on a
 priori knowledge of the study species can be implemented in a diverse
 array of study systems and makes the case for using existing, biologically
 meaningful knowledge about a system to help navigate the myriad of
 methodological decisions about data collection and network inference.
description: The dataset was collected from a population of sociable weavers
 at Benfontein Nature Reserve, situated ca. 6 km south-east of Kimberley,
 in the Northern Cape Province, South Africa. We used artificial feeding
 stations and RFID technology to collect social network data.
description: There are 7 RData files containing the functions and the datasets
 used in the manuscript. There is a dataset for each colony, except colony
 11 and colony 20 that have 2 datasets each (for the 2 different data
 collection setups) as explained in the manuscript.
 There is an R script example that contains all the steps needed
 to replicate the analyses of the manuscript. The script has comments to
 help guide the readers. If you have any questions
 contact: andrem343@hotmail.com or andremcferreira@cibio.up.pt.
DOI: 10.5061/dryad.mgqnk98x6
title: Data set used in Differences in co-divergence reveals that community-wide diversification in the mountains of southwest China during the Pleistocene varied among species

description: Mountains of Southwest China (MSWC) is a biodiversity hotspot with highly
 complex and unusual terrain. However, with the majority of studies
 focusing on the biogeographic consequences of massive mountain building,
 the Quaternary legacy of biodiversity for the MSWC has long been
 overlooked. Here, we took a statistical comparative phylogeography
 approach to examine factors that shaped community-wide diversification.
 With data from 30 vertebrate species, the results reveal spatially
 concordant genetic structure, and temporally clustered co-divergence
 events associated with river barriers during severe glacial cycles. This
 indicates the importance of riverine barriers in the phylogeographic
 history of the MSWC vertebrate community. We conclude that the repeated
 glacial cycles are associated with temporal synchrony of divergence
 patterns that are themselves structured by the heterogeneity of the
 montane landscape has of the MSWC. This orderly process of
 diversifications has profound implications for conservation by
 highlighting the relative independence of different geographic areas in
 which communities have responded similarly to climate changes and calls
 for further comparative phylogeographic investigations to reveal the
 connection between biological traits and divergence pulses in this
 biodiversity hotspot.
DOI: 10.5061/dryad.f4qrfj6tc
title: Lost and found: frogs in a biodiversity hotspot rediscovered with environmental DNA

description: Declines and extinctions are increasing globally and challenging
 conservationists to keep pace with biodiversity monitoring. Organisms
 leave DNA traces in the environment and this free DNA in soil, water, and
 air is referred to as environmental DNA (eDNA). The analysis of eDNA is a
 highly sensitive method with the potential to rapidly assess local
 diversity and the status of threatened species. We searched for DNA traces
 of 30 target amphibian species of conservation concern, at different
 levels of threat, using an environmental DNA metabarcoding approach to
 analyze water samples from six montane sites in the Atlantic Coastal
 Forest and adjacent Cerrado grasslands of Brazil. We successfully detected
 DNA traces of four declined species (Hylodes ornatus, H. regius,
 Crossodactylus timbuhy, and Vitreorana eurygnatha); two locally
 disappeared (Phasmahyla exilis and P. guttata); and one species that has
 not been seen since 1968 (Megaelosia bocainensis). We confirm the presence
 of species undetected by traditional methods, underscoring the efficacy of
 eDNA metabarcoding for biodiversity monitoring at low population
 densities, especially in megadiverse tropical sites, and its potential
 application in conservation biology.
DOI: 10.5061/dryad.x69p8czg2
title: Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs

description: The New World Screwworm fly, Cochliomyia hominivorax, is a major pest of
 livestock in South America and Caribbean. However, few genomic resources
 have been available for this species. A genome of 534 Mb was assembled
 from long read PacBio DNA sequencing of DNA from a highly inbred strain.
 Analysis of molecular evolution identified 40 genes that are likely under
 positive selection. Developmental RNA-seq analysis identified specific
 genes associated with each stage. We identify and analyze the expression
 of genes that are likely important for host-seeking behavior
 (chemosensory), development of larvae in open wounds in warm-blooded
 animals (heat shock protein, immune response) and for building transgenic
 strains for genetic control programs including gene drive (sex
 determination, germline). This study will underpin future experiments
 aimed at understanding the parasitic lifestyle of the screwworm fly and
 greatly facilitate future development of strains for efficient systems for
 genetic control of screwworm.
description: Braker used for gene models.RepeatModeler2 for repetitive
 sequence identification. Blast for chemonsensory, heat shock and immune
 reponse genes.
description: no missing values
DOI: 10.5061/dryad.5mkkwh73c
title: Data from: Understanding the social dynamics of breeding phenology: indirect genetic effects and assortative mating in a long distance migrant

description: Phenological traits, such as the timing of reproduction, are often
 influenced by social interactions between paired individuals. Such partner
 effects may occur when pair members affect each other’s pre-breeding
 environment. Partner effects can be environmentally and/or genetically
 determined, and quantifying direct and indirect genetic effects is
 important for understanding the evolutionary dynamics of phenological
 traits. Here, using 26 years of data from a pedigreed population of a
 migratory seabird, the common tern ( Sterna hirundo ), we investigate male
 and female effects on female laying date. We find that female laying date
 harbors both genetic and environmental variation, and is additionally
 influenced by the environmental, and, to a lower extent, genetic,
 component of her mate. We demonstrate this partner effect to be largely
 explained by male arrival date. Interestingly, analyses of mating patterns
 with respect to arrival date show mating to be strongly assortative and,
 using simulations, we show that this assortative mating for arrival date
 leads to overestimation of partner effects. Our study provides evidence
 for partner effects on breeding phenology in a long distance migrant,
 while uncovering the potential causal pathways underlying the observed
 effects and raising awareness for confounding effects due to assortative
 mating or other common environmental effects.
description: Data used for models presented in:           Understanding the social dynamics of breeding phenology: indirect genetic effects and assortative mating in a long distance migrant by Moiron M., Araya-Ajoy Y.G., Teplitsky C., Bouwhuis S. and Charmantier A.   published in American Naturalist                             for information regarding the analyses, please contact mariamoironc@gmail.com   for information regarding the data, please contact sandra.bouwhuis@ifv-vogelwarte.de if you'd like to use the data, please also contact sandra.bouwhuis@ifv-vogelwarte.de                   these data are part of those collected in an ongoing individual-based longitudinal population study additional data are likely to be available, and we are often very happy to collaborate provided that none of our own staff or students is working on a conflicting project
DOI: 10.7280/d1n96k
title: The sensory basis of schooling by intermittent swimming in the rummy-nose tetra (Hemigrammus rhodostomus) -- [Data analysis]

description: Schooling is a collective behavior that enhances the ability of a fish to
 sense and respond to its environment. Although schooling is essential to
 the biology of a diversity of fishes, it is generally unclear how this
 behavior is coordinated by different sensory modalities. We used
 experimental manipulation and kinematic measurements to test the role of
 vision and flow sensing in the rummy-nose tetra (Hemigrammus rhodostomus),
 which swims with intermittent phases of bursts and coasts. Groups of five
 fish required a minimum level of illuminance (&gt; 1.5 lx) to achieve
 the necessary close nearest-neighbor distance and high polarization for
 schooling. Compromising the lateral line system with an antibiotic
 treatment caused tetras to swim with greater nearest-neighbor distance and
 lower polarization. Therefore, vision is both necessary and sufficient for
 schooling in H. rhodostomus and both sensory modalities aid in attraction.
 These results can serve as a basis for understanding the individual roles
 of sensory modalities in schooling for some fish species.
description: This study considered the sensory basis of schooling by
 experimental manipulation in the rummy-nose tetra (Hemigrammus
 rhodostomus). The role of flow sensing was tested by compromising the
 lateral line system by chemical exposure. The visual system was
 manipulated by varying the intensity of visible light. The effects of
 these manipulations on schooling were assessed with an analysis of the
 kinematics of the swimming in groups of five fish. This repository
 contains the data and scripted code (in MATLAB) to perform all kinematic
 analyses for the study.
description: Familiarity with MATLAB coding is required to perform the
 analysis. The major scripts for data analysis are as follows:
 acqSingle.m - Performs data acquisition for video
 recordings. anaShort.m - Performs the major analysis of
 short-duration experiments. anaLong.m - Performs the
 major anlaysis for long-duration experiments.
 batchMaster.m - Performs analyses on multiple experiments at
 once. The remaining m-files are called from the above
 files for performaning discrete tasks in image processing and data
 analysis.
DOI: 10.5061/dryad.sf7m0cg3m
title: Data from: Effects of soil particles and convective transport on dispersion and aggregation of nanoplastics via small-angle neutron scattering (SANS) and ultra SANS (USANS)

description: Terrestrial nanoplastics (NPs) pose a serious threat to agricultural food
 production systems due to the potential harm of soil-born micro- and
 macroorganisms that promote soil fertility and ability of NPs to adsorb
 onto and penetrate into vegetables and other crops. Very little is known
 about the dispersion, fate and transport of NPs in soils. This is because
 of the challenges of analyzing terrestrial NPs by conventional microscopic
 techniques due to the low concentrations of NPs and absence of optical
 transparency in these systems. Herein, we investigate the potential
 utility of small-angle neutron scattering (SANS) and Ultra SANS (USANS) to
 probe the agglomeration behavior of NPs prepared from polybutyrate adipate
 terephthalate, a prominent biodegradable plastic used in agricultural
 mulching, in the presence of vermiculite, an artificial soil. SANS with
 the contrast matching technique was used to study the aggregation of NPs
 co-dispersed with vermiculite in aqueous media. We determined the contrast
 match point for vermiculite was 66% D 2 O / 33% H 2 O. At this condition,
 the signal for vermiculite was ~50-100%-fold lower that obtained using
 neat H 2 O or D 2 O as solvent. According to SANS and USANS, smaller-sized
 NPs (50 nm) remained dispersed in water and did not undergo size reduction
 or self-agglomeration, nor form agglomerates with vermiculite.
 Larger-sized NPs (300-1000 nm) formed self-agglomerates and agglomerates
 with vermiculite, demonstrating their significant adhesion with soil.
 However, employment of convective transport (simulated by ex situ stirring
 of the slurries prior to SANS and USANS analyses) reduced the
 self-agglomeration, demonstrating weak NP-NP interactions. Convective
 transport also led to size reduction of the larger-sized NPs. Therefore,
 this study demonstrates the potential utility of SANS and USANS with
 contrast matching technique for investigating behavior of terrestrial NPs
 in complex soil systems.
description: For Figures 1 (and S2, which is a replotting of Fig 1 with error
 bars), the data contained were collected at Oak Ridge National Laboratory
 (ORNL), after data reduction as described in the main paper. The
 "info" tab provides information on the SANS and USANS
 instrumentation and when the data was collected. For Figure 2, the same
 comments as given for Fig. 1 apply. The power law fits were obtained via
 standard regression (using the Linest function of Excel. Analyses are not
 shown.) For Figure 3, the same comments as given for Fig. 1 apply. The
 experimental data was obtained by sbtracting the power law fits from the
 SANS and USANS data, both of which are given in Fig. 2. The model fits
 were obtained from performing a form factor model using modeling software
 developed by the National Institute of Standards, National Center for
 Neutron Research (NIST-NCNR) with IGOR-Pro serving as the
 platform.
DOI: 10.5061/dryad.0k6djh9xc
title: The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote skulls

description: Cranial morphology is remarkably varied in living amniotes, ranging from
 short-faced mammals to the elongate snouts of crocodylians. This diversity
 of shapes is thought to correspond with feeding ecology, a relationship
 repeatedly demonstrated at smaller phylogenetic scales, but one that
 remains untested across amniote phylogeny. Using a combination of 2D
 geometric and linear morphometrics, we investigate the links between
 phylogenetic relationships, diet, and skull shape in an expansive dataset
 of extant amniotes with teeth: mammals, lepidosaurs, and crocodylians. We
 find that both phylogeny and diet have statistically significant effects
 on skull shape, although these effects differ depending on the dataset
 analyzed. The three major clades largely partition morphospace, each
 plotting in separate regions with limited overlap. Mammals and squamates
 extensively diversify within their respective regions. Among all three
 groups, dietary generalists often occupy clade-specific central regions of
 morphospace. Some parallel changes in skull shape occur in clades with
 distinct evolutionary histories but similar diets. However, members of a
 given clade often present distinct skull shape solutions for a given diet,
 and the vast majority of species retain the unique aspects of their
 ancestral skull plan, underscoring the limits of morphological convergence
 due to ecology in amniotes. These data demonstrate that certain skull
 shapes may provide functional advantages suited to particular diets, but
 accounting for both phylogenetic history and ecology can provide a more
 nuanced approach for inferring the ecology and functional morphology of
 cryptic or extinct amniotes.
DOI: 10.5061/dryad.kh189323d
title: Data from: REM sleep stabilizes hypothalamic representation of feeding behavior

description: During rapid eye movement (REM) sleep, behavioral
 unresponsiveness contrasts strongly with intense brain-wide neural
 network dynamics. Yet, the physiological functions of
 this cellular activation remain unclear. Using in vivo
 calcium imaging in freely behaving mice, we found that inhibitory
 neurons in the lateral hypothalamus (LHvgat) show unique
 activity patterns during feeding that are reactivated during REM,
 but not NREM, sleep. REM sleep specific optogenetic silencing of
 LHvgat cells induced a re-organization of these activity patterns
 during subsequent feeding behaviors accompanied by decreased food
 intake. Our findings provide evidence for a role for REM
 sleep in the maintenance of cellular representations of
 feeding behavior.
description: The data provided here were collected from <em>in
 vivo</em> calcium imaging of vesicular GABA and glycine-expressing
 neurons in the lateral hypothalamus (LH<sup>vgat</sup>) of
 freely moving mice. The mice were either exploring an open field arena and
 feeding or sleeping in their home cages. The raw data were obtained as
 movies of cellular activity, which were then processed to extract activity
 time series for individual detected cells. The dataset additionally
 features the video tracking of the animals during the open field
 exploration and the respective behavioral scoring as well as EEG and EMG
 data and sleep scoring.
description: All the data are provided as .mat files and explanation to the
 individual variables can be found in READ_ME.txt. Analysis functions and
 scripts are enclosed in a sub-folder next to the data. There is a master
 analysis script (AnalysisTemplate.m) that explains the analyses and calls
 the different functions.
DOI: 10.15468/dl.vgunnm
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000202890, K-M000822728, K-M000769680, K-M000769753, K-M000235257, K-M000036355)"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002431-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ngf1vhhrj
title: Data from: How gut microbiome interactions affect nutritional traits of Drosophila melanogaster

description: Most research on the impact of the gut microbiome on animal nutrition is
 designed to identify the effects of single microbial taxa and single
 metabolites of microbial origin, without considering the potentially
 complex network of interactions among co-occurring microorganisms. Here,
 we investigate how different microbial associations and their fermentation
 products affect host nutrition, using Drosophila melanogaster colonized
 with three gut microorganisms (the bacteria Acetobacter fabarum and
 Lactobacillus brevis and the yeast Hanseniaspora uvarum) in all seven
 possible combinations. Some microbial effects on host traits could be
 attributed to single taxa (e.g. yeast-mediated reduction of insect
 development time), while other effects were sex-specific and driven by
 among-microbe interactions (e.g. male lipid content determined by
 interactions between the yeast and both bacteria). Parallel analysis of
 nutritional indices of microbe-free flies administered different microbial
 fermentation products (acetic acid, acetoin, ethanol and lactic acid)
 revealed a single consistent effect: that the lipid content of both male
 and female flies is reduced by acetic acid. This effect was recapitulated
 in male flies colonized with both yeast and Acetobacter, but not for any
 microbial treatment in females nor in males with other microbial
 complements. These data suggest that the effect of microbial fermentation
 products on host nutritional status is strongly context-dependent, with
 respect to both the combination of associated microorganisms and host sex.
 Taken together, our findings demonstrate that among-microbe interactions
 can play a critically important role in determining the physiological
 outcome of host-microbiome interactions in Drosophila and, likely, in
 other animal hosts.