cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1r3v
title: Data from: Changing measurements or changing movements? Sampling scale and movement model identifiability across generations of biologging technology

description: 1. Animal movement patterns contribute to our understanding of variation
 in breeding success and survival of individuals, and the implications for
 population dynamics. 2. Over time, sensor technology for measuring
 movement patterns has improved. Although older technologies may be
 rendered obsolete, the existing data are still valuable, especially if new
 and old data can be compared to test whether a behavior has changed over
 time. 3. We used simulated data to assess the ability to quantify and
 correctly identify patterns of seabird flight lengths under observational
 regimes used in successive generations of wet/dry logging technology. 4.
 Care must be taken when comparing data collected at differing time-scales,
 even when using inference procedures that incorporate the observational
 process, as model selection and parameter estimation may be biased. In
 practice, comparisons may only be valid when degrading all data to match
 the lowest resolution in a set. 5. Changes in tracking technology, such as
 the wet/dry loggers explored here, that lead to aggregation of
 measurements at different temporal scales make comparisons challenging. We
 therefore urge ecologists to use synthetic data to assess whether accurate
 parameter estimation is possible for models comparing disparate data sets
 before planning experiments and conducting analyses such as responses to
 environmental changes or the assessment of management actions.
description: dry segment data from
 flights of Antarctic albatrossesSee README file for data
 informationalbatross_drysegments.csvImplementation of the negative log likelihood - 1992 style loggersThis file implements the negative log-likelihood corresponding to the 1992-style immersion loggers. The file includes examples of fitting parameters of this distribution to flight data. requires "shifted_dists.R"mle_1992.RImplementation of the negative log likelihood - 2004 style loggersThis file implements the negative log-likelihood corresponding to the 2004-style immersion loggers. The file includes examples of fitting parameters of this distribution to flight data. requires "shifted_dists.R"mle_2004.Rshifted_distsImplementation of the shifted gamma, shifted exponential, pareto, and q-exponential distributions.model selection for albatross dataThis file implements the model fitting and model selection procedure for the albatross data found in "albatross_drysegments.csv". Requires: mle_1992.R; mle_2004.R; shifted_dists.Robs_model_select.R
DOI: 10.5281/zenodo.18382243
title: Reconstructed 3H charge structure: Insights from Patterson function analysis

description: Charge structure of tritium (³H) is reconstructed via Patterson function analysis.
DOI: 10.5281/zenodo.18382244
title: Reconstructed 3H charge structure: Insights from Patterson function analysis

description: Charge structure of tritium (³H) is reconstructed via Patterson function analysis.
DOI: 10.5061/dryad.c682f
title: Data from: Genetic structure of native ant supercolonies varies in space and time

description: Ant supercolonies are the largest cooperative units known in nature. They
 consist of networks of interconnected nests with hundreds of reproductive
 queens, where individuals move freely between nests, cooperate across nest
 boundaries and show little aggression towards non-nestmates. The
 combination of high queen numbers and free mixing of workers, queens and
 brood between nests results in extremely low nestmate relatedness. In such
 low-relatedness societies, cooperative worker behaviour appears
 maladaptive because it may aid random individuals instead of relatives.
 Here, we provide a comprehensive picture of genetic substructure in
 supercolonies of the native wood ant Formica aquilonia using traditional
 population genetic as well as network analysis methods. Specifically, we
 test for spatial and temporal variation in genetic structure of different
 classes of individuals within supercolonies and analyse the role of worker
 movement in determining supercolony genetic networks. We find that
 relatedness within supercolonies is low but positive when viewed on a
 population level, which may be due to limited dispersal of individuals
 and/or ecological factors such as nest site limitation and competition
 against conspecifics. Genetic structure of supercolonies varied with both
 sample class and sampling time point, which indicates that mobility of
 individuals varies according to both caste and season and suggests that
 generalizing has to be carried out with caution in studies of
 supercolonial species. Overall, our analysis provides novel evidence that
 native wood ant supercolonies exhibit fine-scale genetic substructure,
 which may explain the maintenance of cooperation in these low-relatedness
 societies.
description: Genotypes from two
 Formica aquilonia supercoloniesMYLA_allSamples_Genotypes.txt
DOI: 10.5061/dryad.b354f
title: Data from: Morphological diversification of ampullariid gastropods (Nsungwe Formation, late Oligocene, Rukwa Rift Basin, Tanzania) is coincident with onset of East African rifting

description: A new freshwater gastropod fauna is described from the late Oligocene
 Nsungwe Formation of the Rukwa Rift Basin, Tanzania. Six new species of
 ampullariids are established including five species of Lanistes (L.
 microovum, L. nsungwensis, L. songwellipticus, L. songweovum and L.
 rukwaensis) and one species of Carnevalea (C. santiapillai). These taxa
 occupy a morphospace region comparable to nearly half of extant Lanistes,
 a common and widespread genus in Africa and Madagascar. Palaeoecological
 evidence indicates that Nsungwe ampullariids inhabited fluvial, pond, and
 paludal environments. Among these species are the oldest high-spired and
 fluvially adapated Lanistes taxa. We suggest that Nsungwe Lanistes rapidly
 diversified in concert with habitat heterogeneity associated with the
 initiation of rifting along the Western Branch of the East African Rift
 System (EARS). Taxonomy, evolution and the biogeographic affinities of
 Nsungwe Formation freshwater gastropods contributes significantly to
 expanding the undersampled Palaeogene invertebrate fossil record of
 continental Africa.
description: Supplementary
 TablesSet of data tables of
 specimen numbers and measurements. Table S1. Complete list of Nsungwe
 Formation ampullariid specimens. Table S2. Descriptive data for Nsungwe
 Formation ampullariids. Table S3. Descriptive data for comparative
 ampullariids. Table S4. Morphometric data for Nsungwe Formation
 ampullariids included in PCA analysis. Table S5. Morphometric data for
 comparative specimens included in PCA analysis.AppendixTables.xlsxSupplementary FigureFigure S1. PCA results showing morphospace occupation for Nsungwe Formation ampullariids when analyzed separately from the comparison species set. Biplot indicates vectors of Total shell height (H); Total shell width (D), Aperture height (h), and Spire height (S).NsungweOnlyPCA-FigS1.pdf
DOI: 10.5061/dryad.087b9
title: Data from: Egg size investment in superb fairy-wrens: helper effects are modulated by climate

description: Natural populations might exhibit resilience to changing climatic
 conditions if they already show adaptive flexibility in their reproductive
 strategies. In cooperative breeders, theory predicts that mothers with
 helpers should provide less care when environmental conditions are
 favourable, but maintain high investment when conditions are challenging.
 Here, we test for evidence of climate-mediated flexibility in maternal
 investment in the cooperatively breeding superb fairy-wren Malurus
 cyaneus. We focus on egg size because in this species egg size influences
 offspring size, and females reduce egg investment when there are helpers
 at the nest. We report that females lay larger eggs during dry, hot
 conditions. However, the effect of temperature is modulated by the
 presence of helpers: the average egg size of females with helpers is
 reduced during cooler conditions but increased during hot conditions
 relative to females without helpers. This appears to reflect plasticity in
 egg investment rather than among female differences. Analysis of maternal
 survival suggests that helped females are better able to withstand the
 costs of breeding in hot conditions than females without helpers. Our
 study suggests that females can use multiple, independent cues to modulate
 egg investment flexibly in a variable environment.
description: Egg data for
 DryadOutput from climwin
 analysesClimwin and female
 survival for DryadOutput from climwin
 analysis and female survival data
DOI: 10.5061/dryad.vg89038
title: Data from: Local adaptation reduces the metabolic cost of environmental warming

description: Metabolism shapes the ecosystem role of organisms by dictating their
 energy demand and nutrient recycling potential. Metabolic theory (MTE)
 predicts consumer metabolic and recycling rates will rise in a warming
 world, especially if body size declines, but it ignores potential for
 adaptation. We measured metabolic and nutrient excretion rates of
 individuals from populations of a globally invasive fish that recently
 colonized a wide temperature range (19-37°C) on two continents. Fish body
 size declined across our temperature gradient and MTE predicted large
 rises in population energy demand and nutrient recycling. However, we
 found that the allometry and temperature dependency of metabolism varied
 in a countergradient pattern with local temperature in a way that offset
 predictions of MTE. Scaling of nutrient excretion was more variable, and
 did not track temperature. Our results suggest that adaptation can reduce
 the metabolic cost of warming, increasing the prospects for population
 persistence under extreme warming scenarios.
description: Gambusia affinis
 metbolic, excretion, and size dataField metabolic rate,
 excretion rate, and seine data from 10 field sites.Dryad
 data.xlsx
DOI: 10.5061/dryad.vn6dv
title: Data from: Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon

description: Commensal microbes, whether they are beneficial or pathogenic, are
 sensitive to host processes that starve or swamp the prokaryote with large
 fluctuations in local zinc concentration. To understand how microorganisms
 coordinate a dynamic response to changes in zinc availability at the
 molecular level, we evaluated the molecular mechanism of the zinc-sensing
 zinc uptake regulator (Zur) protein at each of the known Zur-regulated
 genes in Escherichia coli. We solved the structure of zinc-loaded Zur
 bound to the PznuABC promoter and show that this metalloregulatory protein
 represses gene expression by a highly cooperative binding of two adjacent
 dimers to essentially encircle the core element of each of the
 Zur-regulated promoters. Cooperativity in these protein-DNA interactions
 requires a pair of asymmetric salt bridges between Arg52 and Asp49′ that
 connect otherwise independent dimers. Analysis of the protein-DNA
 interface led to the discovery of a new member of the Zur-regulon: pliG.
 We demonstrate this gene is directly regulated by Zur in a zinc responsive
 manner. The pliG promoter forms stable complexes with either one or two
 Zur dimers with significantly less protein-DNA cooperativity than observed
 at other Zur regulon promoters. Comparison of the in vitro Zur-DNA binding
 affinity at each of four Zur-regulon promoters reveals ca. 10,000-fold
 variation Zur-DNA binding constants. The degree of Zur repression observed
 in vivo by comparison of transcript copy number in wild-type and Δzur
 strains parallels this trend spanning a 100-fold difference. We conclude
 that the number of ferric uptake regulator (Fur)-family dimers that bind
 within any given promoter varies significantly and that the thermodynamic
 profile of the Zur-DNA interactions directly correlates with the
 physiological response at different promoters.
description: Gilston_etal_2014_Figure
 3Raw
 data files from Figure 3 A and DGilston_etal_2014_Figure
 4Raw
 data from Gel-shift data in Figure 4Gilston_etal_2014_Figure
 5Raw
 data from gel-shift experiments in Figure 5Gilston_etal_2014_Figure
 6Raw
 data from Gel-shift experiments in Figure 6, includes additional Hill
 Plots references in manuscriptGilston_etal_2014_Figure
 S3Summary of raw data from
 Figure S3 Native gel shift experiments using varying percentages of
 acrylamideGilston_etal_2014_Figure
 S4Raw
 data from Hill plot Figure S4Gilston_etal_2014_Figure
 S5Raw
 data used for mutant gel-shift analysis in Figure S5Gilston_etal_2014_Figure
 S6Raw
 data from major and minor groove width Curves analysis from Figure
 S6Gilston_etal_2014_Figure
 S7Raw
 data from gel-shift of pliG data in Figure S7Gilston_etal_2014_Table
 3Raw
 data from data summarized in Table 3
DOI: 10.5061/dryad.dj3v81b
title: Data from: Honey bee (Apis mellifera) sociability and nestmate affiliation is dependent on the social environment experienced post-eclosion

description: Underpinning the formation of a social group is the motivation of
 individuals to aggregate and interact with conspecifics, termed
 sociability. Here we developed an assay, inspired by vertebrate approaches
 to evaluate social behaviours, to simultaneously examine the development
 of honey bee (Apis mellifera) sociability and nestmate affiliation. Focal
 bees were placed in a testing chamber, which was separated from groups of
 nestmates and conspecific non-nestmates by single-layer mesh screens.
 Assessing how much time bees spent contacting the two mesh screens allowed
 us to quantify simultaneously how much bees sought proximity and
 interaction with other bees, and their preference for nestmates over
 non-nestmates. Both sociability and nestmate affiliation could be detected
 soon after emergence as an adult. Isolation early in adult life impaired
 honey bee sociability but there was no evidence for a critical period for
 the development of the trait since isolated bees exposed to their hive for
 24 hours when as old as 6 days still recovered high levels of sociability.
 Our data show that even for advanced social insects, sociability is a
 developmental phenomenon and experience-dependent.
description: JEBbeesocprefdata for bee sociality scoresJEBbeedyadlikelihooddata for bee dyadic interactions
DOI: 10.5061/dryad.4f0d1
title: Data from: Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito

description: Human-aided transport is responsible for many contemporary species
 introductions, yet the contribution of human-aided transport to dispersal
 within non-native regions is less clear. Understanding dispersal dynamics
 for invasive species can streamline mitigation efforts by targeting routes
 that contribute disproportionally to spread. Because of its limited
 natural dispersal ability, rapid spread of the Asian tiger mosquito (Aedes
 albopictus) has been attributed to human-aided transport, but until now
 the relative roles of human-aided and natural movement have not been
 rigorously evaluated. Here, we use landscape genetics and
 information-theoretic model selection to evaluate 52 models representing
 9,240 pair-wise dispersal paths among sites across the US range for Ae.
 albopictus, and show that recent gene flow reflects a combination of
 natural and human-aided dispersal. Highways and water availability
 facilitate dispersal at a broad spatial scale, but gene flow is hindered
 by forests at the current distributional limit (range-edge) and by
 agriculture among sites within the mosquito's native climatic niche
 (range-core). Our results show that highways are important to genetic
 structure between range-edge and range-core pairs, suggesting a role for
 human-aided mosquito transport to the range edge. In contrast, natural
 dispersal is dominant at smaller spatial scales, reflecting a shifting
 dominance to natural movement two decades after introduction. These
 conclusions highlight the importance of: (a) early intervention for
 species introductions, particularly those with readily dispersed dormant
 stages and short generation times, and (b) strict monitoring of commercial
 shipments for transported immature stages of Ae. albopictus, particularly
 towards the northern edge of the US range.
description: Genotype data for Medley
 et al. 2014genotypes.txt includes
 individual genotypes for each of 9 loci and 26 locations. In final
 analyses, one locus (Ap2) was removed due to null alleles, and four sites
 were removed because of non-independence to result in 22
 sites.genotypes.txtMedley_etalMOLECOLdataMRDMSite-level data, including genetic and landscape distances for Medley et al. 2014.ScriptForDryadAUG2014Script for running MRDM analyses for Medley et al. 2014.
DOI: 10.5061/dryad.6444j
title: Data from: Synergetic use of Sentinel-1 and Sentinel-2 for assessments of heathland conservation status

description: Habitat quality assessments often demand wall-to-wall information about
 the state of vegetation. Remote sensing can provide this information by
 capturing optical and structural attributes of plant communities. Although
 active and passive remote sensing approaches are considered as
 complementary techniques, they have been rarely combined for conservation
 mapping. Here, we combined spaceborne multispectral Sentinel-2 and
 Sentinel-1 SAR data for a remote sensing-based habitat quality assessment
 of dwarf shrub heathland, which was inspired by nature conservation field
 guidelines. Therefore, three earlier proposed quality layers representing
 (1) the coverage of the key dwarf shrub species, (2) stand structural
 diversity and (3) an index reflecting co-occurring vegetation were mapped
 via linking in situ data and remote sensing imagery. These layers were
 combined in an RGB-representation depicting varying stand attributes,
 which afterwards allowed for a rule-based derivation of pixel-wise habitat
 quality classes. The links between field observations and remote sensing
 data reached correlations between 0.70 and 0.94 for modeling the single
 quality layers. The spatial patterns shown in the quality layers and the
 map of discrete quality classes were in line with the field observations.
 The remote sensing based mapping of heathland conservation status showed
 an overall agreement of 76% with field data. Transferring the approach in
 time (applying a second set of Sentinel 1 and 2 data) caused a decrease in
 accuracy to 73%. Our findings suggest that Sentinel-1 SAR contains
 information about vegetation structure that is complimentary to optical
 data and therefore relevant for nature conservation. While we think that
 rule-based approaches for quality assessments offer the possibility for
 gaining acceptance in both communities applied conservation and remote
 sensing, there is still need for developing more robust and transferable
 methods.
description: Schmidt_et_al_RSECSupplementary material
DOI: 10.6084/m9.figshare.31149463
title: <b>Conservation Blind Spot: The Critical Role of Larval Stage in Assessing Extinction Risk-Code and original data</b>

description: In an era of severe global biodiversity threats, understanding the link between species' traits and their endangerment helps uncover causes of risk and infer threats to understudied species. Most animals have complex life cycles with distinct stages that may face stage-specific threats. Current conservation frameworks rely heavily on adult traits, potentially misjudging extinction risk. Using Chinese anurans as a model, we integrated functional traits from both adult and tadpole stages to examine their association with extinction risk. We found that body size positively correlates with risk in both stages. Lentic microhabitat use reduces risk in tadpoles but shows no significant link in adults. Adult relative tympanum diameter and head length also correlate with extinction risk. These results indicate that species vulnerability is shaped by multi-stage traits, with both shared and stage-specific threats. Conservation based solely on adult traits may fail to accurately assess species threats. We call for integrating a whole-life-history perspective into biodiversity assessment and conservation to more effectively address the global biodiversity crisis.
DOI: 10.6084/m9.figshare.31149463.v2
title: <b>Conservation Blind Spot: The Critical Role of Larval Stage in Assessing Extinction Risk-Code and original data</b>

description: In an era of severe global biodiversity threats, understanding the link between species' traits and their endangerment helps uncover causes of risk and infer threats to understudied species. Most animals have complex life cycles with distinct stages that may face stage-specific threats. Current conservation frameworks rely heavily on adult traits, potentially misjudging extinction risk. Using Chinese anurans as a model, we integrated functional traits from both adult and tadpole stages to examine their association with extinction risk. We found that body size positively correlates with risk in both stages. Lentic microhabitat use reduces risk in tadpoles but shows no significant link in adults. Adult relative tympanum diameter and head length also correlate with extinction risk. These results indicate that species vulnerability is shaped by multi-stage traits, with both shared and stage-specific threats. Conservation based solely on adult traits may fail to accurately assess species threats. We call for integrating a whole-life-history perspective into biodiversity assessment and conservation to more effectively address the global biodiversity crisis.
DOI: 10.6084/m9.figshare.31149463.v1
title: <b>Conservation Blind Spot: The Critical Role of Larval Stage in Assessing Extinction Risk</b>

description: In an era of severe global biodiversity threats, understanding the link between species' traits and their endangerment helps uncover causes of risk and infer threats to understudied species. Most animals have complex life cycles with distinct stages that may face stage-specific threats. Current conservation frameworks rely heavily on adult traits, potentially misjudging extinction risk. Using Chinese anurans as a model, we integrated functional traits from both adult and tadpole stages to examine their association with extinction risk. We found that body size positively correlates with risk in both stages. Lentic microhabitat use reduces risk in tadpoles but shows no significant link in adults. Adult relative tympanum diameter and head length also correlate with extinction risk. These results indicate that species vulnerability is shaped by multi-stage traits, with both shared and stage-specific threats. Conservation based solely on adult traits may fail to accurately assess species threats. We call for integrating a whole-life-history perspective into biodiversity assessment and conservation to more effectively address the global biodiversity crisis.