cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p86t5
title: Data from: Spending limited resources on de-extinction could lead to net biodiversity loss

description: There is contentious debate surrounding the merits of de-extinction as a
 biodiversity conservation tool. Here, we use extant analogues to predict
 conservation actions for potential de-extinction candidate species from
 New Zealand and the Australian state of New South Wales, and use a
 prioritization protocol to predict the impacts of reintroducing and
 maintaining populations of these species on conservation of extant
 threatened species. Even using the optimistic assumptions that
 resurrection of species is externally sponsored, and that actions for
 resurrected species can share costs with extant analogue species, public
 funding for conservation of resurrected species would lead to fewer extant
 species that could be conserved, suggesting net biodiversity loss. If full
 costs of establishment and maintenance for resurrected species populations
 were publicly funded, there could be substantial sacrifices in extant
 species conservation. If conservation of resurrected species populations
 could be fully externally sponsored, there could be benefits to extant
 threatened species. However, such benefits would be outweighed by
 opportunity costs, assuming such discretionary money could directly fund
 conservation of extant species. Potential sacrifices in conservation of
 extant species should be a crucial consideration in deciding whether to
 invest in de-extinction or focus our efforts on extant species.
description: NSW dataset and code for
 prioritizationCode and database for
 New South Wales prioritization. See ReadMe file for additional details,
 and see NZ dataset and code ReadMe
 (http://datadryad.org/resource/doi:10.5061/dryad.3qn55) for details on
 code design.NSW for
 DRYAD.zip
DOI: 10.5061/dryad.c7c8f
title: Data from: Genome-wide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River

description: The lower Congo River (LCR) is a freshwater biodiversity hotspot in Africa
 characterized by some of the world's largest rapids. However, little
 is known about the evolutionary forces shaping this diversity, which
 include numerous endemic fishes. We investigated phylogeographic
 relationships in Teleogramma, a small clade of rheophilic cichlids, in the
 context of regional geography and hydrology. Previous studies have been
 unable to resolve phylogenetic relationships within Teleogramma due to
 lack of variation in nuclear genes and discrete morphological characters
 among putative species. To sample more broadly across the genome we
 analyzed double-digest restriction-associated sequencing (ddRAD) data from
 53 individuals across all described species in the genus. We also assessed
 body shape and mitochondrial variation within and between taxa.
 Phylogenetic analyses reveal previously unrecognized lineages and
 instances of microallopatric divergence across as little as ~1.5 km.
 Species ranges appear to correspond to geographic regions broadly
 separated by major hydrological and topographic barriers, indicating these
 features are likely important drivers of diversification. Mitonuclear
 discordance indicates one or more introgressive hybridization events, but
 no clear evidence of admixture is present in nuclear genomes, suggesting
 these events were likely ancient. A survey of female fin patterns hints
 that previously undetected lineage-specific patterning may be acting to
 reinforce species cohesion. These analyses highlight the importance of
 hydrological complexity in generating diversity in certain freshwater
 systems, as well as the utility of ddRAD-Seq data in understanding
 diversification processes operating both below and above the species
 level.
description: SNP data from ddRAD
 sequencingVCF file containing
 reference-aligned SNPs (single nucleotide polymorphisms) across
 Teleogramma specimens.teleo_refalign_full.vcfMorphometric dataMorphometric data including PC scores, covariance matrix, and procrustes coordinates.PC scores, CovMatrix, Procrustes coordinates.txt
DOI: 10.5061/dryad.n9f77
title: Data from: Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models

description: Pairwise maximum-entropy models have been used in neuroscience to predict
 the activity of neuronal populations, given only the time-averaged
 correlations of the neuron activities. This paper provides evidence that
 the pairwise model, applied to experimental recordings, would produce a
 bimodal distribution for the population-averaged activity, and for some
 population sizes the second mode would peak at high activities, that
 experimentally would be equivalent to 90% of the neuron population active
 within time-windows of few milliseconds. Several problems are connected
 with this bimodality: 1. The presence of the high-activity mode is
 unrealistic in view of observed neuronal activity and on neurobiological
 grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise
 maximum-entropy distribution cannot be found: in fact, Boltzmann learning
 would produce an incorrect distribution; similarly, common variants of
 mean-field approximations also produce an incorrect distribution. 3. The
 Glauber dynamics associated with the model is unrealistically bistable and
 cannot be used to generate realistic surrogate data. This bimodality
 problem is first demonstrated for an experimental dataset from 159 neurons
 in the motor cortex of macaque monkey. Evidence is then provided that this
 problem affects typical neural recordings of population sizes of a couple
 of hundreds or more neurons. The cause of the bimodality problem is
 identified as the inability of standard maximum-entropy distributions with
 a uniform reference measure to model neuronal inhibition. To eliminate
 this problem a modified maximum-entropy model is presented, which reflects
 a basic effect of inhibition in the form of a simple but non-uniform
 reference measure. This model does not lead to unrealistic bimodalities,
 can be found with Boltzmann learning, and has an associated Glauber
 dynamics which incorporates a minimal asymmetric inhibition.
description: Rostamietal_after_second_revision.tarThe folder includes all script and data necessary to reproduce the figures in the associated publication: "Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models".
DOI: 10.5061/dryad.v4f53
title: Data from: Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns

description: In conservation studies, solely widespread species are often used as
 indicators of diversity patterns, but narrow-ranged species can show
 different patterns. Here, we assess how well subsets of narrow-ranged,
 widespread or randomly selected plant species represent patterns of
 species richness and weighted endemism in Gabon, tropical Africa.
 Specifically, we assess the effect of using different definitions of
 widespread and narrow-ranged and of the information content of the
 subsets. Finally, we test if narrow-ranged species are overrepresented in
 species-rich areas. Based on distribution models of Gabonese plant
 species, we defined sequential subsets from narrow-ranged-to-widespread,
 widespread-to-narrow-ranged, and 100 randomly arranged species sequences
 using the range sizes of species in tropical Africa and within Gabon.
 Along these sequences, correlations between subsets and the total species
 richness and total weighted endemism patterns were computed. Random
 species subsets best represent the total species richness pattern, whereas
 subsets of narrow-ranged species best represent the total weighted
 endemism pattern. For species ordered according to their range sizes in
 tropical Africa, subsets of narrow-ranged species represented the total
 species richness pattern better than widespread species subsets did.
 However, the opposite was true when range sizes were truncated by the
 Gabonese national country borders. Correcting for the information content
 of the subset results in a skew of the sequential correlations, its
 direction depending on the range-size frequency distribution. Finally, we
 find a strong, positive, non-linear relation between weighted endemism and
 total species richness. Observed differences in the contribution of
 narrow-ranged, widespread and randomly selected species to species
 richness and weighted endemism patterns can be explained by the range-size
 frequency distribution and the use of different definitions of widespread
 or narrow-ranged. We call for a reconsideration of the use of widespread
 species as an indicator of diversity patterns, and advocate using the full
 ranges of species when assessing diversity patterns.
description: vanProosdij_etal_2016_PlosOne_SMTable_specieslistThis file lists all species for which significant Species Distribution Models were generated that were used for analysis. The SDMs of these species are uploaded here as well.vanProosdij_etal_2016_PlosOne_SpeciesDistributionModelsThese files are the Species Distribution Models for 2089 Gabonese plant species that were trained on sufficient observation records and perform signifincantly better than random null models. Files were cropped to the country borders of Gabon and are presented in .asc format.
DOI: 10.5061/dryad.5jc0t
title: Data from: Behavioral response to song and genetic divergence in two subspecies of white-crowned sparrows (Zonotrichia leucophrys)

description: Divergence in sexual signals may drive reproductive isolation between
 lineages, but behavioral barriers can weaken in contact zones. Here, we
 investigate the role of song as a behavioral and genetic barrier in a
 contact zone between two subspecies of white-crowned sparrows (Zonotrichia
 leucophrys). We employed a reduced genomic dataset to assess population
 structure and infer the history underlying divergence, gene flow and
 hybridization. We also measured divergence in song and tested behavioral
 responses to song using playback experiments within and outside the
 contact zone. We found that the subspecies form distinct genetic clusters,
 and demographic inference supported a model of secondary contact. Song
 phenotype, particularly length of the first note (a whistle), was a
 significant predictor of genetic subspecies identity and genetic distance
 along the hybrid zone, suggesting a close link between song and genetic
 divergence in this system. Individuals from both parental and admixed
 localities responded significantly more strongly to their own song than to
 the other subspecies song, supporting song as a behavioral barrier.
 Putative parental and admixed individuals were not significantly different
 in their strength of discrimination between own and other songs; however,
 individuals from admixed localities tended to discriminate less strongly,
 and this difference in discrimination strength was explained by song
 dissimilarity as well as genetic distance. Therefore, we find that song
 acts as a reproductive isolating mechanism that is potentially weakening
 in a contact zone between the subspecies. Our findings also support the
 hypothesis that intra-specific song variation can reduce gene flow between
 populations.
description: SNP calls for
 Zonotrichia leucophrys nuttalli x Z. l. pugetensis hybrid
 zoneDataset includes 6419
 SNP loci for 169 individuals across the Zonotrichia leucophrys nuttalli x
 Z. l. pugetensis hybrid zone. Sampling information, including individual
 ID, locality, lat/long, sex, and whether song data is available is also
 provided. Songs are archived at the Borror Laboratory of Bioacoustics at
 Ohio State University.Zonotrichia_SNPs_6419loci_169ind.xlsx
DOI: 10.5061/dryad.7d6c5
title: Data from: The neuroendocrine immunomodulatory axis-like pathway mediated by circulating haemocytes in pacific oyster Crassostrea gigas

description: The neuroendocrine-immune (NEI) regulatory network is a complex system,
 which plays an indispensable role in the immunity of host. In this study,
 a neuroendocrine immunomodulatory axis (NIA)-like pathway mediated by the
 nervous system and haemocytes was characterized in the oyster Crassostrea
 gigas. Once invaded pathogen was recognized by the host, the nervous
 system would temporally release neurotransmitters to modulate the immune
 response. Instead of acting passively, oyster haemocytes were able to
 mediate neuronal immunomodulation promptly by controlling the expression
 of specific neurotransmitter receptors on cell surface and modulating
 their binding sensitivities, thus regulating intracellular concentration
 of Ca2+. This neural immunomodulation mediated by the nervous system and
 haemocytes could influence cellular immunity in oyster by affecting mRNA
 expression level of TNF genes, and humoral immunity by affecting the
 activities of key immune-related enzymes. In summary, though simple in
 structure, the ‘nervous-haemocyte’ NIA-like pathway regulates both
 cellular and humoral immunity in oyster, meaning a world to the effective
 immune regulation of the NEI network.
description: Figure and
 TableFigures &
 Tables
DOI: 10.5061/dryad.97vq0
title: Data from: Metabolic characterization of intact cells reveals intracellular amyloid beta but not its precursor protein to reduce mitochondrial respiration

description: One hallmark of Alzheimer´s disease are senile plaques consisting of
 amyloid beta (Aβ), which derives from the processing of the amyloid
 precursor protein (APP). Mitochondrial dysfunction has been linked to the
 pathogenesis of Alzheimer´s disease and both Aβ and APP have been reported
 to affect mitochondrial function in isolated systems. However, in intact
 cells, considering a physiological localization of APP and Aβ, it is
 pending what triggers the mitochondrial defect. Thus, the aim of this
 study was to dissect the impact of APP versus Aβ in inducing mitochondrial
 alterations with respect to their subcellular localization. We performed
 an overexpression of APP or beta-site amyloid precursor protein cleaving
 enzyme 1 (BACE1), increasing APP and Aβ levels or Aβ alone, respectively.
 Conducting a comprehensive metabolic characterization we demonstrate that
 only APP overexpression reduced mitochondrial respiration, despite lower
 extracellular Aβ levels compared to BACE overexpression. Surprisingly,
 this could be rescued by a gamma secretase inhibitor, oppositionally
 indicating an Aβ-mediated mitochondrial toxicity. Analyzing Aβ
 localization revealed that intracellular levels of Aβ and an increased
 spatial association of APP/Aβ with mitochondria are associated with
 reduced mitochondrial respiration. Thus, our data provide marked evidence
 for a prominent role of intracellular Aβ accumulation in Alzheimer´s
 disease associated mitochondrial dysfunction. Thereby it highlights the
 importance of the localization of APP processing and intracellular
 transport as a decisive factor for mitochondrial function, linking two
 prominent hallmarks of neurodegenerative diseases.
description: raw data, Schaefer et
 al.raw data, uncropped
 blotsraw_data_Schaefer_et_al.zip
DOI: 10.5061/dryad.v1t1b
title: Data from: Relative advantages of dichromatic and trichromatic color vision in camouflage breaking

description: There is huge diversity in visual systems and color discrimination
 abilities, thought to stem from an animal’s ecology and life history. Many
 primate species maintain a polymorphism in color vision, whereby most
 individuals are dichromats but some females are trichromats, implying that
 selection sometimes favors dichromatic vision. Detecting camouflaged prey
 is thought to be a task where dichromatic individuals could have an
 advantage. However, previous work either has not been able to disentangle
 camouflage detection from other ecological or social explanations, or did
 not use biologically relevant cryptic stimuli to test this hypothesis
 under controlled conditions. Here, we used online “citizen science” games
 to test how quickly humans could detect cryptic birds (incubating
 nightjars) and eggs (of nightjars, plovers and coursers) under
 trichromatic and simulated dichromatic viewing conditions. Trichromats had
 an overall advantage, although there were significant differences in
 performance between viewing conditions. When searching for consistently
 shaped and patterned adult nightjars, simulated dichromats were more
 heavily influenced by the degree of pattern difference than were
 trichromats, and were poorer at detecting prey with inferior pattern and
 luminance camouflage. When searching for clutches of eggs—which were more
 variable in appearance and shape than the adult nightjars—the simulated
 dichromats learnt to detect the clutches faster, but were less sensitive
 to subtle luminance differences. These results suggest there are
 substantial differences in the cues available under viewing conditions
 that simulate different receptor types, and that these interact with the
 scene in complex ways to affect camouflage breaking.
description: Click
 DataSpreadsheets contain
 click-data for our two online games. One for the adult nightjar-finding
 game, and the other for the clutch-finding game. Files are
 CSVs.
DOI: 10.5061/dryad.94kt2
title: Data from: Comparative system identification of flower tracking performance in three hawkmoth species reveals adaptations for dim light vision

description: Flight control in insects is heavily dependent on vision. Thus, in dim
 light, the decreased reliability of visual signal detection also prompts
 consequences for insect flight. We have an emerging understanding of the
 neural mechanisms that different species employ to adapt the visual system
 to low light. However, much less explored are comparative analyses of how
 low light affects the flight behaviour of insect species, and the
 corresponding links between physiological adaptations and behaviour. We
 investigated whether the flower tracking behaviour of three hawkmoth
 species with different diel activity patterns revealed luminance-dependent
 adaptations, using a system identification approach. We found clear
 luminance-dependent differences in flower tracking in all three species,
 which were explained by a simple luminance-dependent delay model, which
 generalized across species. We discuss physiological and anatomical
 explanations for the variance in tracking responses, which could not be
 explained by such simple models. Differences between species could not be
 explained by the simple delay model. However, in several cases, they could
 be explained through the addition on a second model parameter, a simple
 scaling term, that captures the responsiveness of each species to flower
 movements. Thus, we demonstrate here that much of the variance in the
 luminance-dependent flower tracking responses of hawkmoths with different
 diel activity patterns can be captured by simple models of neural
 processing.
description: dataTracks_XXX.XLS contains
 the raw digitized data from 100 fps videos of moths tracking the robotic
 flower. Luminance levels are indicated in the filenames, species are
 abbreviated as M (Macroglossum stellatarum), Ma (Manduca sexta) and D
 (Deilephila elpenor). Each set of four columns is data from one video with
 the X,Y points for the flower and the moth respectively. Videos were
 either 10s or 20 seconds long for a total of 1000 or 2000 rows.
 ANALYSIS_XXX.xls is a matrix containing the processed tracking data from
 each of the moth species (names indicated in filename). Columns are as
 follows: First: An integer identifier for each individual moth (same as
 trial). Second: The component frequency of the command flower movement
 (0.2-13.7 Hz for each moth). Third: luminance condition (1-3, code
 explained in the column header). Fourth: The gain of the moth at that
 frequency (a gain of 1 indicates the same amplitude tracking). Fifth: The
 phase of the moth w.r.t. the flower at that frequency in radians. Data
 were unwrapped as described in the methods. Sixth: Tracking error as
 calculated in the paper. Seventh: The complex valued response of the moth
 with respect to the flower.
DOI: 10.5061/dryad.2t3t7
title: Data from: Prediction limits of mobile phone activity modelling

description: Thanks to their widespread usage, mobile devices have become one of the
 main sensors of human behaviour and digital traces left behind can be used
 as a proxy to study urban environments. Exploring the nature of the
 spatio-temporal patterns of mobile phone activity could thus be a crucial
 step towards understanding the full spectrum of human activities. Using 10
 months of mobile phone records from Greater London resolved in both space
 and time, we investigate the regularity of human telecommunication
 activity on urban scales. We evaluate several options for decomposing
 activity timelines into typical and residual patterns, accounting for the
 strong periodic and seasonal components. We carry out our analysis on
 various spatial scales, showing that regularity increases as we look at
 aggregated activity in larger spatial units with more activity in them. We
 examine the statistical properties of the residuals and show that it can
 be explained by noise and specific outliers. Also, we look at sources of
 deviations from the general trends, which we find to be explainable based
 on knowledge of the city structure and places of attractions. We show
 examples how some of the outliers can be related to external factors such
 as specific social events.
description: Shared dataset
 supporting the paperData sharable under
 agreement with the data provider. Basic description is
 included.predictability_paper_shared_data.zip
DOI: 10.5061/dryad.737gk
title: Data from: Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure

description: Ecological data often show temporal, spatial, hierarchical (random
 effects), or phylogenetic structure. Modern statistical approaches are
 increasingly accounting for such dependencies. However, when performing
 cross-validation, these structures are regularly ignored, resulting in
 serious underestimation of predictive error. One cause for the poor
 performance of uncorrected (random) cross-validation, noted often by
 modellers, are dependence structures in the data that persist as
 dependence structures in model residuals, violating the assumption of
 independence. Even more concerning, because often overlooked, is that
 structured data also provides ample opportunity for overfitting with
 non-causal predictors. This problem can persist even if remedies such as
 autoregressive models, generalized least squares, or mixed models are
 used. Block cross-validation, where data are split strategically rather
 than randomly, can address these issues. However, the blocking strategy
 must be carefully considered. Blocking in space, time, random effects or
 phylogenetic distance, while accounting for dependencies in the data, may
 also unwittingly induce extrapolations by restricting the ranges or
 combinations of predictor variables available for model training, thus
 overestimating interpolation errors. On the other hand, deliberate
 blocking in predictor space may also improve error estimates when
 extrapolation is the modelling goal. Here, we review the ecological
 literature on non-random and blocked cross-validation approaches. We also
 provide a series of simulations and case studies, in which we show that,
 for all instances tested, block cross-validation is nearly universally
 more appropriate than random cross-validation if the goal is predicting to
 new data or predictor space, or for selecting causal predictors. We
 recommend that block cross-validation be used wherever dependence
 structures exist in a dataset, even if no correlation structure is visible
 in the fitted model residuals, or if the fitted models account for such
 correlations.
description: ECOG-02881.R1Appendix 6 - R code and data for case studies and simulations (as presented in Boxes 1-4 in manuscript).