cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2753k
title: Data from: Coexistence of evolving bacteria stabilized by a shared Black Queen function

description: The Black Queen Hypothesis (BQH) was originally proposed to explain the
 dependence of some marine bacteria on helper organisms for protection from
 hydrogen peroxide (HOOH). The BQH predicts that selection for the
 evolutionary loss of leaky functions from individuals can produce
 commensal or mutualistic interactions. We demonstrated the leakiness of
 HOOH detoxification by complementing a HOOH-sensitive Escherichia coli
 mutant with a plasmid-encoded HOOH-detoxifying enzyme, KatG, and then
 evolving populations founded by this strain in two environments. When HOOH
 was absent, plasmid-carrying cells were outcompeted by plasmid-free
 segregants, reflecting the high cost of KatG expression. However,
 plasmid-carrying and plasmid-free cells coexisted for at least 1,200
 generations in three replicate populations evolved in the presence of
 HOOH, although their relative proportions fluctuated as beneficial
 mutations arose in one type or the other. Evolved plasmid-bearing cells
 reduced the cost of plasmid carriage even as they increased the rate of
 HOOH removal relative to the ancestor. Meanwhile, plasmid-free cells
 remained dependent on HOOH detoxification by the plasmid-bearing cells.
 These results demonstrate that partitioning of a Black Queen function can
 enable the stable coexistence of very similar organisms, even in this most
 restrictive case where the two types are competing for a single resource.
description: MorrisBQH2014This file contains all the data, code, and instructions necessary to recreate the figures and analyses contained in the associated manuscript. Full descriptions of the files' contents can be found in the readme.txt file contained within the zip archive.MorrisBQH.zip
DOI: 10.5061/dryad.1vd07
title: Data from: Superb fairy-wrens respond more to alarm calls from mate and kin compared to unrelated individuals

description: Variation in the acoustic structure of alarm signals has mainly been
 viewed as coding information about the type of predator or the level of
 threat posed by the predator. Alarm signals can also convey individuality
 information, but whether conspecifics use this information and the
 function of individually distinct alarm calls remains unclear. In this
 study, we examined whether mobbing alarm calls of superb fairy-wrens
 (Malurus cyaneus) communicated information about sex, individual identity
 or kinship and whether this information was stable between years. We then
 examined the discriminative abilities of adults using playback
 experiments. We first used a habituation/dishabituation procedure to
 investigate whether adults were able to differentiate between two
 unfamiliar individuals. Then, we tested whether they adjusted their
 response based on their level of familiarity or kinship with the caller by
 comparing their response to mobbing alarm calls of their mate, a first
 order relative from the same population, an unrelated individual from the
 same population, or a distant bird from a different population. Superb
 fairy-wren mobbing alarm calls conveyed information about individuality,
 but not sex or kinship, and vocal individuality varied between years.
 Adults discriminated between two unfamiliar individuals and responded more
 strongly to playback of calls from their mate and kin versus individuals
 from another population. We discussed the conditions for discrimination
 based on individual characteristics rather than categories of individuals.
description: Colombelli-Negrel &
 Evans Mobbing alarm calls dataThis data file contains
 data from call analysis and playback trials conducted in the field on
 superb fairy-wrens in Cleland, South Australia.The data contains the full
 details of each call recorded, including sex of the individual, individual
 number, order of year recorded, and all call parameters measured as well
 as the full details of each playback trial conducted including subject
 info, playback stimulus info, and response of the
 subject
DOI: 10.5061/dryad.12gh2
title: Data from: Genetic population structure in prickly sculpin (Cottus asper) reflects isolation by environment between two life history ecotypes

description: Life-history transitions have evolved repeatedly in numerous taxa,
 although the ecological and evolutionary conditions favouring such
 transitions in the presence of gene flow remain poorly understood. The
 present study aimed to disentangle the effects of isolation-by-distance
 and isolation-by-environment on genetic differentiation between two
 sympatric life-history ecotypes. Using 14 microsatellite loci, we first
 characterized amphidromous and freshwater groups of Cottus asper in a high
 gene flow setting in the Lower Fraser River system (south-western British
 Columbia, Canada) to test for the effects of habitat and geographical
 distance on the distribution of life-history ecotypes. Within the main
 river channel, no genetic differentiation was found, whereas tributaries
 even close to the estuary were genetically differentiated. Partial mantel
 tests confirmed that genetic differentiation between river tributaries and
 the main channel was independent from geographical distance, with
 distance-scaled migration rates indicating reduced gene flow from the main
 channel into the tributaries. Our results suggest that
 isolation-by-environment can play an important role for the early stage of
 life-history transitions, and may promote differentiation among
 life-history ecotypes despite the presence of gene flow.
description: CottusAsper_microsatellitelociGenepop datafile for 14 microsatellite loci genotyped for Cottus asper in southwestern British Columbia.DRYAD_popgen_CottusAsper.gen
DOI: 10.6084/m9.figshare.31049932
title: Hecke–Lerch Correspondence VII: Master Dataset of 33,824 Number Fields with Universal Archimedean Kernel Verification and Class Field Generation

description: This dataset accompanies <b>Paper VII of the Hecke–Lerch Correspondence series</b>, which resolves the long-standing “Regulator Gap” problem in explicit analytic class field theory for number fields of degree n&gt;2<i>n</i>&gt;2. It contains verification results for <b>33,824 quadratic and cyclic cubic number fields</b>, including:
DOI: 10.6084/m9.figshare.31049932.v1
title: Hecke–Lerch Correspondence VII: Master Dataset of 33,824 Number Fields with Universal Archimedean Kernel Verification and Class Field Generation

description: This dataset accompanies <b>Paper VII of the Hecke–Lerch Correspondence series</b>, which resolves the long-standing “Regulator Gap” problem in explicit analytic class field theory for number fields of degree n&gt;2<i>n</i>&gt;2. It contains verification results for <b>33,824 quadratic and cyclic cubic number fields</b>, including:
DOI: 10.5061/dryad.d8p66
title: Data from: Neural correlations enable invariant coding and perception of natural stimuli in weakly electric fish

description: Neural representations of behaviorally relevant stimulus features
 displaying invariance with respect to different contexts are essential for
 perception. However, the mechanisms mediating their emergence and
 subsequent refinement remain poorly understood in general. Here, we
 demonstrate that correlated neural activity allows for the emergence of an
 invariant representation of natural communication stimuli that is further
 refined across successive stages of processing in the weakly electric fish
 Apteronotus leptorhynchus. Importantly, different patterns of input
 resulting from the same natural communication stimulus occurring in
 different contexts all gave rise to similar behavioral responses. Our
 results thus reveal how a generic neural circuit performs an elegant
 computation that mediates the emergence and refinement of an invariant
 neural representation of natural stimuli that most likely constitutes a
 neural correlate of perception.
description: behavior
 databehavior data files,
 please unzip and look at readme file first.behavior.zipdual recordingssimultaneous recordings from afferent pairs. Unzip then look at readme filedual_recordings.zipmidbrain electrophysiological recordingsElectrophysiological data from midbrain neuronsmidbrain_final_new.zipsingle afferent electrophysiological recordingsData from single afferents. Please look at readme file first.single_recordings_new.zipanalysis filesMatlab codes used for analysis. Please look at readme file first.analysis_files.ziphindbrain electrophysiological recordingsHindbrain electrophysiological recordings, please look at readme file first.hindbrain_electrophysiological_recordings.zip
DOI: 10.15468/dl.aab4u3
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sessea stipulata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 54 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001001-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rm228
title: Data from: Variation in the ecstatic display call of the Gentoo Penguin (Pygoscelis papua) across regional geographic scales

description: Geographic variation in bird vocalizations is common and has been
 associated with genetic differences and speciation, as well as with
 short-term changes in response to anthropogenic noise. Because
 vocalizations are used for individual recognition in many species,
 geographic variation in these traits may affect mate choice, pair bonding,
 and territory defense. Anecdotal evidence suggests the existence of
 geographic variation in vocalizations between isolated populations of
 Gentoo Penguins (Pygoscelis papua), but there have been no comprehensive
 studies of Gentoo Penguin vocalizations across a broad geographic range.
 We used acoustic recordings of ambient colony sound at 22 breeding
 colonies in the Antarctic Peninsula and South Shetland Islands, South
 Georgia, the Falkland Islands, and Argentina to address 2 main questions
 regarding Gentoo Penguin vocalizations: (1) How do ecstatic display calls
 vary both within and between individuals, colonies, and regions? (2) Can
 ecstatic display calls be used to distinguish subspecies? We found high
 levels of variation between individuals and between colonies, but little
 additional variation between regions or subspecies. We found no trends to
 suggest a latitudinal gradient in vocal characteristics, although we did
 find that some measures varied with relative distance between colonies.
 Although we found significant differences at the colony level, unknown
 calls could not easily be categorized to colony or region by machine
 learning. We conclude that the vocal soundscape of each colony is driven
 by variation between individuals within a colony and, developing
 independently from neighboring colonies, becomes differentiated from other
 colonies through a process of drift. Although individual calls could, in
 most cases, be identified to subspecies by machine learning, our analysis
 suggests that subspecies differences may be driven by variation among
 colonies and that subspecies identification may be unreliable using
 acoustics alone.
description: South Georgia, Falklands
 & ArgentinaAudio recordings from
 eight sites in South Georgia, the Falkland Islands, and
 ArgentinaSouth
 Georgia_Falklands_Argentina.zipAntarctic
 Peninsula_1Audio recordings from
 seven sites along the Antarctic PeninsulaAntarctic
 Peninsula_2Audio recordings from
 seven sites along the Antarctic PeninsulaREADME
DOI: 10.15468/dl.vdmh3d
title: Occurrence Download

description: A dataset containing 88467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.18.6_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 88467 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000992-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.10rn5
title: Data from: Motion analysis of non-model organisms using a hierarchical model: influence of setup enclosure dimensions on gait parameters of Swinhoe’s striped squirrels as a test case

description: In in-vivo motion analyses, data from a limited number of subjects and
 trials is used as proxy for locomotion properties of entire populations,
 yet the inherent hierarchy of the individual and population level is
 usually not accounted for. Despite the increasing availability of
 hierarchical model frameworks for statistical analyses, they have not been
 applied extensively to comparative motion analysis. As a case study for
 the use of hierarchical models, we analyzed locomotor parameters of four
 Swinhoe’s striped squirrels. The small-bodied arboreal mammals exhibit
 brief bouts of rapid asymmetric gaits. Spatio-temporal parameters on
 runways with experimentally varied dimensions of the setup enclosure were
 compared to test for its potentially confounding effects. We applied
 principal component analysis to evaluate changes to the overall locomotor
 pattern. A common, non-hierarchical, pooled statistical analysis of the
 data revealed significant differences in some of the parameters depending
 on enclosure dimensions. In contrast, we used a hierarchical Bayesian
 generalized linear model (GLM) that considers subject specific differences
 and population effects to compare the effect of enclosure dimensions on
 the measured parameters and the principal components. None of the
 population effects were confirmed by the hierarchical GLM. The confounding
 effect of a single subject that deviates in its locomotor behavior is
 potentially bigger than the influence of the experimental variation in
 enclosure dimensions. Our findings justify the common practice of
 researchers to intuitively select an enclosure with dimensions assumed as
 “non-constraining”. Hierarchical models can easily be designed to cope
 with limited sample size and bias introduced by deviating behavior of
 individuals. When limited data is available—a typical restriction of
 in-vivo motion analyses of non-model organisms—density distributions of
 the Bayesian GLM used here remain reliable and the hierarchical structure
 of the model optimally exploits all available information. We provide code
 to be adjusted to other research questions.
description: Mielke et
 al_ESM_codeCode for the statistical
 analysis of kinematic data using a hierarchical Bayesian generalized
 linear model as described in Mielke et al. "Motion analysis of
 non-model organisms using a hierarchical model: Influence of setup
 enclosure size on gait parameters of Swinhoe’s striped squirrels as a test
 case".Mielke et
 al_ESM_dataA table containing all
 data to reproduce the analysis as described in Mielke et al. "Motion
 analysis of non-model organisms using a hierarchical model: Influence of
 setup enclosure size on gait parameters of Swinhoe’s striped squirrels as
 a test case".
DOI: 10.15468/dl.t94ud2
title: Occurrence Download

description: A dataset containing 1078 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((89.26650 19.51472,131.73350 19.51472,131.73350 36.48528,89.26650 36.48528,89.26650 19.51472))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Macaca thibetana",
 "Year 1932-2025"
 ]
}

 The dataset includes 1078 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001002-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.21jf0t1
title: Data from: Mate choice in the eye and ear of the beholder? Female multimodal sensory configuration influences her preferences

description: A common assumption in sexual selection studies is that receivers decode
 signal information similarly. However, receivers may vary in how they rank
 signallers if signal perception varies with an individual’s sensory
 configuration. Furthermore, receivers may vary in their weighting of
 different elements of multimodal signals based on their sensory
 configuration. This could lead to complex levels of selection on
 signalling traits. We tested whether multimodal sensory configuration
 could affect preferences for multimodal signals. We used brown-headed
 cowbird (Molothrus ater) females to examine how auditory sensitivity and
 auditory filters, which influence auditory spectral and temporal
 resolution, affect song preferences, and how visual spatial resolution and
 visual temporal resolution, which influence resolution of a moving visual
 signal, affect visual display preferences. Our results show that
 multimodal sensory configuration significantly affects preferences for
 male displays: females with better auditory temporal resolution preferred
 songs that were shorter, with lower Wiener entropy, and higher frequency;
 and females with better visual temporal resolution preferred males with
 less intense visual displays. Our findings provide new insights into
 mate-choice decisions and receiver signal processing. Furthermore, our
 results challenge a longstanding assumption in animal communication which
 can affect how we address honest signalling, assortative mating, and
 sensory drive.
description: Female mating
 preferences and sensory processingData is sorted by female
 (N=20) and trial date; each line has listed the two dependent factors we
 analyzed (CSD duration and CSD latency) and the 4 physiological parameters
 we assessed (auditory sensitivity, auditory equivalent rectangular
 bandwidth of the auditory filters, photoreceptor densities, and flicker
 fusion frequency).NewDataforDryad.xlsx
DOI: 10.5061/dryad.v8q6c
title: Data from: Extra-group mating increases inbreeding risk in a cooperatively breeding bird

description: In many cooperatively-breeding species females mate extra-group, the
 adaptive value of which remains poorly understood. One hypothesis posits
 that females employ extra-group mating to access mates whose genotypes are
 more dissimilar to their own than their social mates’, so as to increase
 offspring heterozygosity. We test this hypothesis using life-history and
 genetic data from 36 cooperatively-breeding white-browed sparrow weaver
 (Plocepasser mahali) groups. Contrary to prediction, a dominant female’s
 relatedness to her social mate did not drive extra-group mating decisions
 and, moreover, extra-group mating females were significantly more related
 to their extra-group sires than their social mates. Instead, dominant
 females were substantially more likely to mate extra-group when paired to
 a dominant male of low heterozygosity, and their extra-group mates
 (typically dominants themselves) were significantly more heterozygous than
 the males they cuckolded. The combined effects of mating with extra-group
 males of closer relatedness but higher heterozygosity resulted in
 extra-group-sired offspring that were no more heterozygous than their
 within-group-sired half-siblings. Our findings are consistent with a role
 for male-male competition in driving extra-group mating and suggest that
 the local kin structure typical of cooperative breeders could counter
 potential benefits to females of mating extra-group by exposing them to a
 risk of inbreeding.
description: HetSim function for
 Simulating Offspring HeterozygosityHetSim function for
 Dryad.RWhite-Browed Sparrow
 Weaver GenotypesAssembled Genotypes
 v2.txtR Code for Analysis of
 Paired Data by Randomisation TestPaired T Randomisation
 .RMean Heterozygosity by
 Locus Data for HetSim functionMean Heterozygosity by
 Locus.csv
DOI: 10.5061/dryad.7jq46
title: Data from: Early accumulation of active fraction soil carbon in newly established cellulosic biofuel systems

description: We examined relative changes in soil C pools shortly after the
 establishment of six perennial and two annual bioenergy cropping systems
 that differed in diversity (monoculture vs. polyculture). Perennial
 systems included two monocultures (switchgrass, Panicum virgatum; and
 miscanthus, Miscanthus × giganteus) and four polycultures including hybrid
 poplar (Populus sp.) + herbaceous understory; mixed native grasses,
 successional vegetation, and restored prairie. Two annual systems included
 no-till continuous corn (Zea mays) and rotational corn (corn-soybean
 (Glycine max)-canola (Brassica napus)). Each crop was planted in a full
 factorial design at both a moderate fertility Alfisol and a high fertility
 Mollisol site. Relative differences in active, slow, and passive C pools
 in surface soils, where C changes are most likely to be detected early,
 were evaluated with 322-day laboratory incubations followed by acid
 hydrolysis to infer different pools from exponential decay curves. Five
 years post-establishment, active C pools under perennial polycultures at
 the Alfisol site were up to twice those under annual and perennial
 monocultures, and followed the order hybrid poplars (696 ± 216 μg C g− 1
 soil, n = 5 replicate blocks) ≈ native grasses (656 ± 155) ≈ restored
 prairie (638 ± 44) &gt; early successional (500 ± 54) ≫ continuous
 corn (237 ± 68) ≈ rotational corn (180 ± n.a.). Active C pools in
 perennial monocultures were similar to those in continuous corn:
 switchgrass (274 ± 29) ≈ miscanthus (299 ± 9). In contrast, differences in
 active C pools among crops at the more fertile Mollisol site were not
 detectable except for greater pools in the restored prairie and rotational
 corn systems. At both sites, slow and passive C pools differed little
 among systems except that slow pools were greater in the poplar system.
 That diversity rather than perenniality itself led to greater active C
 pools suggests that polycultures might be used to accelerate soil C
 accumulation in bioenergy and other perennial cropping systems.
description: Sprunger_Robertson_2018_Geoderma_Dryad