cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b341k
title: Data from: A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

description: Background: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped
 bacterium was discovered in the lungs of a dead parakeet (Melopsittacus
 undulatus) that was kept in captivity in a petshop in Basel, Switzerland.
 The organism is described with a chemotaxonomic profile and the nearly
 complete genome sequence obtained through the assembly of short sequence
 reads. Results: Genome sequence analysis and characterization of
 respiratory quinones, fatty acids, polar lipids, and biochemical phenotype
 is presented here. Comparison of gene sequences revealed that the most
 similar species is Pelistega europaea, with BLAST identities of only 93%
 to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC
 content (~43%) as the organism isolated from the parakeet, DSM 24701
 (40%). The closest full genome sequences are those of Bordetella spp. and
 Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa
 platform were assembled with the Edena de novo assembler to form 195
 contigs comprising the ~2 Mb genome. Genome annotation with RAST,
 construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence
 and the rpoB gene, and phylogenetic placement using other highly conserved
 marker genes with ML Tree all suggest that the bacterial species belongs
 to the Alcaligenaceae family. Analysis of samples from cages with healthy
 parakeets suggested that the newly discovered bacterial species is not
 widespread in parakeet living quarters. Conclusions: Classification of
 this organism in the current taxonomy system requires the formation of a
 new genus and species. We designate the new genus Basilea and the new
 species psittacipulmonis. The type strain of Basilea psittacipulmonis is
 DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number
 JX412111 and GI 406042063).
description: 16S rDNA Neighbor
 Joining Tree, Nexus formatNJ_16S.nexusrpoB neighbor joining tree, Nexus formatNJ_rpoB.nexus
DOI: 10.18167/dvn1/8rkhfx
title: Profitability assessment of the Coffee agroforestry business driven clusters (CaFC)

description: The profitability assessment is based on data on costs and yields per hectare for the F1 hybrid variety 'Starmaya' and a local variety.
DOI: 10.5061/dryad.t2ch6
title: Data from: Parenting behaviour is highly heritable in male stickleback

description: Parental care is critical for fitness, yet little is known about its
 genetic basis. Here, we estimate the heritability of parenting behaviour
 in a species famous for its diversity and its behavioural repertoire:
 three-spined stickleback (Gasterosteus aculeatus). Male threespined
 stickleback are the sole providers of paternal care that is necessary for
 offspring survival, therefore this system offers the opportunity to study
 the inheritance of parental behavior when selection is primarily acting on
 males. Fanning behaviour is a conspicuous parental behaviour that is
 readily quantified in this species. We show that the heritability of
 fanning behaviour is ≥0.9, and significantly different from zero within a
 freshwater population. Moreover, there was abundant genetic variation for
 fanning behaviour, indicating that it could readily evolve. These results
 suggest that parenting behaviour is tractable for further genetic
 dissection in this system.
description: Parenting Heritability
 Data and Analysis Files4 data files, a metadata
 file describing the columns in these files, and an analysis script file
 that can be used to recreate all analyses and figures.Parenting
 Heritability.zip
DOI: 10.18160/6arv-14r6
title: Biogenic in-situ observations (L2), Munich LAI, 2024-04-08–2024-08-14

description: Leaf Area Index (LAI) data from Munich, Germany. Details of the measurements, file contents etc are described in ICOS Cities deliverable report D3.13.
DOI: 10.5061/dryad.9v9d3
title: Data from: Camouflaged or tanned: plasticity in freshwater snail pigmentation

description: By having phenotypically plastic traits, such as morphology, behaviour and
 life history, many organisms optimise their fitness in response to
 fluctuating threats. Freshwater snails with translucent shells, e.g.
 snails from the Radix genus, differ considerably in their mantle
 pigmentation patterns, with snails from the same water body ranging from
 completely dark pigmented to only a few dark patterns. These pigmentation
 differences have previously been suggested to be genetically fixed, but we
 suggest that this polymorphism is due to phenotypic plasticity in response
 to a fluctuating environment. Hence, we here aimed at assessing if common
 stressors, including ultraviolet radiation (UVR) and predation, induce a
 plastic response in mantle pigmentation patterns of Radix balthica. We
 show, in contrast to previous studies, that snails are plastic in their
 expression of mantle pigmentation in response to changes in UVR and
 predator threats, i.e. differences among species or populations are not
 genetically fixed. When exposed to cues from visually hunting fish, R.
 balthica increased the proportion of their dark pigmentation, suggesting a
 crypsis strategy. Snails increased their pigmentation even further in
 response to UVR, but this also lead to reduced complexity of the patterns.
 Furthermore, when exposed to UVR and fish, snails responded in the same
 way as in the UVR treatment, suggesting a trade-off between
 photoprotection and crypsis.
description: Pigmentation and index
 of roundness measurementsbiology letters
 data.txt
DOI: 10.5061/dryad.vj72f
title: Data from: The tonic immobility test: do wild and captive Golden Mantella frogs (Mantella aurantiaca) have the same response?

description: Adaptations to captivity that reduce fitness are one of many reasons,
 which explain the low success rate of reintroductions. One way of testing
 this hypothesis is to compare an important behavioural response in captive
 and wild members of the same species. Thanatosis, is an anti-predator
 strategy that reduces the risk of death from predation, which is a common
 behavioral response in frogs. The study subjects for this investigation
 were captive and wild populations of Mantella aurantiaca. Thanatosis
 reaction was measured using the Tonic Immobility (TI) test, a method that
 consists of placing a frog on its back, restraining it in this position
 for a short period of time and then releasing it and measuring how much
 time was spent feigning death. To understand the pattern of reaction time,
 morphometric data were also collected as body condition can affect the
 duration of thanatosis. The significantly different TI times found in this
 study, one captive population with shorter responses, were principally an
 effect of body condition rather than being a result of rearing
 environment. However, this does not mean that we can always dismiss the
 importance of rearing environment in terms of behavioural skills
 expressed.
description: Mantella_TIData on TI responses from captive and wild golden mantellaData_Matella_TI.txtSVL_GoldenMantellasGolden Mantellas' length measurements
DOI: 10.5281/zenodo.18392194
title: Electron density and molecular electrostatic potential of water dimer
DOI: 10.5281/zenodo.18392195
title: Electron density and molecular electrostatic potential of water dimer
DOI: 10.5061/dryad.gn6qb
title: Data from: Species distributions, quantum theory, and the enhancement of biodiversity measures

description: Species distributions are typically represented by records of their
 observed occurrence at a given spatial and temporal scale. Such records
 are inevitably incomplete and contingent on the spatial-temporal
 circumstances under which the observations were made. Moreover, organisms
 may respond differently to similar environmental conditions at different
 places or moments, so their distribution is, in principle, not completely
 predictable. We argue that this uncertainty exists, and warrants
 considering species distributions as analogous to coherent quantum
 objects, whose distributions are better described by a wavefunction rather
 than by a set of locations. We use this to extend the existing concept of
 "dark diversity", which incorporates into biodiversity metrics
 those species that could, but which have not yet been observed to, inhabit
 a region-thereby developing the idea of "potential
 biodiversity". We show how conceptualizing species'
 distributions in this way could help overcome important weaknesses in
 current biodiversity metrics, both in theory and by using a worked case
 study of mammal distributions in Spain over the last decade. We propose
 that considerable theoretical advances could eventually be gained through
 interdisciplinary collaboration between biogeographers and quantum
 physicists.
description: onlineAppendix1R functions used to calculate the geometric mean of favourabilities (equation 3) and its increment (equation 4)
DOI: 10.5061/dryad.jd8vg
title: Data from: Standard sister clade comparison fails when testing derived character states

description: Comparing species richness in sister clades that differ in a character is
 one of the ways to study factors influencing diversification. While most
 of its applications focused on traits that increase diversification, some
 were used to study the association of a trait with less species richness,
 e.g. the occurrence of dioecy in flowering plants. We show here, using
 simulations and an analytical model, that the null expectation of equal
 species richness that is generally used in sister clade comparisons is
 wrong in the case of a derived trait occurring independently from
 speciation: one should expect less species in the clade with the derived
 character when there is no difference in diversification rates. This is
 due to the waiting time for the derived state to appear, which causes it
 to occur more often on longer branches. This has the important implication
 that the probability for a clade to possess the derived state depends on
 the tree geometry, and thus on species richness: less species-rich clades
 are more likely to possess the derived state. A test for differences in
 species richness should be based upon observed tree imbalance. We present
 a method to do this, and find that we cannot confirm earlier work that
 concluded that dioecy decreases diversification; on the contrary, it seems
 to be associated to higher species richness than expected.
description: scc_examplesExamples of the resampling test for sister clade comparison. Needs data files from the archive data.tar.gz.20131125_scc_examples.Rdata.tar.gzExamples of data found in the literature that can be analysed with the resampling test for sister clade comparisons: 1) viviparity in actinopterygian fishes (from Slowinski and Guyer, 1993, dataset from Lydeard, 1993), 2) dioecy in angiosperms (updated dataset from Heilbuth, 2000)scc_testR source code for the resampling test for sister clade comparisons proposed in the manuscript
DOI: 10.5061/dryad.tp24j18
title: Data from: Response to short-term deprivation of the human adult visual cortex measured with 7T BOLD

description: Sensory deprivation during the post-natal "critical period"
 leads to structural reorganization of the developing visual cortex. In
 adulthood, the visual cortex retains some flexibility and adapts to
 sensory deprivation. Here we show that short-term (2h) monocular
 deprivation in adult humans boosts the BOLD response to the deprived eye,
 changing ocular dominance of V1 vertices, consistent with homeostatic
 plasticity. The boost is strongest in V1, present in V2, V3 &V4
 but absent in V3a and hMT+. Assessment of spatial frequency tuning in V1
 by a population Receptive-Field technique shows that deprivation primarily
 boosts high spatial frequencies, consistent with a primary involvement of
 the parvocellular pathway. Crucially, the V1 deprivation effect correlates
 across participants with the perceptual increase of the deprived eye
 dominance assessed with binocular rivalry, suggesting a common origin. Our
 results demonstrate that visual cortex, particularly the ventral pathway,
 retains a high potential for homeostatic plasticity in the human adult.
description: Data from: Response to
 short-term deprivation of the human adult visual cortex measured with 7T
 BOLDLarge .mat file
 (readable from matlab) holding all the fMRI and psychophysical data
 reported in the manuscript. see readme file for details on how variables
 are formatted and what information is stored in each of
 them.alldata_anonymized.mat
DOI: 10.5061/dryad.k4c21
title: Data from: Information-mediated Allee effects in breeding habitat selection

description: Social information is used widely in breeding habitat selection and
 provides an efficient means for individuals to select habitat; however,
 the population-level consequences of this process are not well explored.
 At low population densities, efficiencies may be reduced because there are
 insufficient ‘information providers’ as cues for high-quality habitat.
 This constitutes what we term an ‘information-mediated Allee effect’. We
 present the first general model for an information-mediated Allee effect
 applied to breeding habitat selection, and unify personal and social
 information, Allee effects, and ecological traps into a common framework.
 In a second model, we consider an explicit mechanism of social information
 gathering through prospecting on conspecific breeding performance. In each
 model, we independently vary personal and social information use to
 demonstrate how dependency on social information may result in either weak
 or strong Allee effects that, in turn, affect population extinction risk.
 Abrupt transitions between outcomes can occur through reduced information
 transfer or small changes in habitat composition. Overall,
 information-mediated Allee effects may produce positive feedbacks that
 amplify population declines in species that are already experiencing
 environmentally-driven stressors, such as habitat loss and degradation.
 Alternatively, social information has the capacity to rescue populations
 from ecological traps.
description: Matlab code for the
 basic Allee modelBasic_Allee_model.mMatlab code for the social prospecting modelProspecting_Allee_model.m
DOI: 10.5061/dryad.221t6
title: Data from: A century-long genetic record reveals that protist effective population sizes are comparable to those of macroscopic species

description: Effective population size (Ne) determines the rate of genetic drift and
 the relative influence of selection over random genetic changes. While
 free-living protist populations characteristically consist of huge numbers
 of cells (N), the absence of any estimates of contemporary Ne raises the
 question whether protist effective population sizes are comparably large.
 Using microsatellite genotype data of strains derived from revived cysts
 of the marine dinoflagellate Pentapharsodinum dalei from sections of a
 sediment record that spanned some 100 years, we present the first
 estimates of contemporary Ne for a local population in a free-living
 protist. The estimates of Ne are relatively small, on the order of a few
 100 individuals, and thus are similar in magnitude to values of Ne
 reported for multicellular animals: the implications are that Ne of P.
 dalei is many orders of magnitude lower than the number of cells present
 (Ne/N~10-12) and that stochastic genetic processes may be more prevalent
 in protist populations than previously anticipated.
description: Pdalei_Msat_GenotypesMicrosatellite genotypes (at six loci) for strains of the marine dinoflagellate P.dalei. Each sample represents the strains that could be revived from a slice of sediment core taken from Koljo Fjord, Sweden.Pdalei_GenotypeData.txt
DOI: 10.82294/dvnwkykns
title: Entrevistas semiestructuradas. Territorio: Cali. Sector: Educación. Año: 2024

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2024, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Educación (educación formal) en la ciudad de Cali.
DOI: 10.5061/dryad.6fd34vr
title: Data from: Alternative reproductive tactics and lifetime reproductive success in a polygynandrous mammal

description: The widespread occurrence of alternative reproductive tactics (ARTs)
 highlights the diverse ways in which sexual selection can operate within a
 population. We studied ARTs in Columbian ground squirrels (Urocitellus
 columbianus), evaluating paternity, lifetime reproductive success, and
 life histories. Reproductively mature male Columbian ground squirrels
 displayed either a territorial or satellite (non-territorial) tactic.
 Territorial males secured a higher proportion of copulations, were more
 likely to mate at earlier positions in females’ mating sequences and sired
 more offspring than satellite males. The tactic males adopted was largely
 a function of weight, age, and experience, with larger, older and more
 experienced males displaying the territorial tactic. At two years of age,
 males adopted the satellite tactic or deferred breeding for the season.
 Two-year-old satellite males were heavier than males that deferred
 breeding, but by age three there was no difference between their weights.
 Males that deferred breeding either adopted the satellite or territorial
 tactic in the following year, with the lighter males displaying the
 satellite tactic. The ARTs that males adopted at two and three years of
 age led to alternative life history pathways. Males that deferred breeding
 and only adopted the territorial tactic during their lifetime had twice
 the number of lifetime offspring compared to males that adopted the
 satellite tactic and then switched to territorial behavior in following
 years, although this difference was not statistically significant. Our
 findings show that the satellite tactic results in lower reproductive
 output both within a single year, except at age two, and over their
 lifetime.
description: Data for ARTs and
 lifetime reproductive success in male CGSMale Columbian ground
 squirrels (Urocitellus columbianus) data collected in the field located in
 Kananaskis Country, Alberta, Canada. Two separate data sets were used for
 the different analyses. Data for the direct comparison between satellite
 and territorial males is in the tab labeled "Direct_Comparison".
 The data for the lifetime reproductive success analysis is in the tab
 labeled "Life_History".Data_ARTs_and_Lifetime_Reproductive_Success_in_CGS.xls
DOI: 10.5061/dryad.6fv96
title: Data from: Does personality affect the ability of individuals to track and respond to changing conditions?

description: One possibility for why individual differences in behavioral plasticity
 are frequently associated with differences in personality might be that
 variation in personality is functionally related to variation in
 cognition. Evidence supporting a link between personality and cognition,
 however, is still limited and contradictory. In this study, we then
 conducted a laboratory experiment with zebra finches (Taeniopygia guttata)
 aimed at examining the role of cognition in shaping individual differences
 in contextual plasticity (i.e., plasticity in behavior between contexts).
 Specifically, we measured neophobia by quantifying the latency of the
 birds to eat near a novel object in two different environments across a
 social gradient and assessed their learning performance on two
 discriminant tasks and a reversal task. In agreement with our expectation,
 we found that less neophobic individuals were less plastic in their
 responses compared to more neophobic ones. Less neophobic individuals were
 also faster to reach the learning criterion but only in the less difficult
 discriminant task they performed first. On the contrary, although we found
 evidence for individual consistency in learning performances, differences
 among individuals in the number of trials needed to pass the task in both
 the more difficult discriminant and reversal tasks were not associated
 with individual differences in neophobia. Thus, our findings indicate that
 individual differences in contextual plasticity do not necessarily result
 from some individuals being more sensitive to environmental changes.
 Instead, we suggest that differences among individuals in their level of
 plasticity might result from differences in the number of suitable
 habitats they may occupy.
description: Data used for the
 stepwise regression analysesPaper_datadryad_personality_and_plasticity.txtData used for the linear mixed effects analysesPaper_datadryad_personality_and_plasticity_neoOnly.txt
DOI: 10.5061/dryad.664cp
title: Data from: Heme pathway evolution in kinetoplastid protists

description: Background: Kinetoplastea is a diverse protist lineage composed of several
 of the most successful parasites on Earth, organisms whose metabolisms
 have coevolved with those of the organisms they infect. Parasitic
 kinetoplastids have emerged from free-living, non-pathogenic ancestors on
 multiple occasions during the evolutionary history of the group.
 Interestingly, in both parasitic and free-living kinetoplastids, the heme
 pathway—a core metabolic pathway in a wide range of organisms—is
 incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far
 seem to bypass the need for heme biosynthesis by acquiring heme or
 intermediate metabolites directly from their environment. Results: Here we
 report the existence of a complete heme biosynthetic pathway in Perkinsela
 spp., kinetoplastids that live as obligate endosymbionts inside
 amoebozoans belonging to the genus Paramoeba. We also use phylogenetic
 analysis to infer the evolution of the heme pathway in Kinetoplastea.
 Conclusion: We show that Perkinsela spp. is a deep-branching kinetoplastid
 lineage, and that lateral gene transfer has played a role in the evolution
 of heme biosynthesis in Perkinsela spp. and other Kinetoplastea. We also
 discuss the significance of a complete heme pathway in Perkinsela as it
 relates to its endosymbiotic relationship with Paramoeba.
description: sequence_alignedThis file contain all the sequences for each trees in separate file.sequences_aligned.7zsequence_aligned_and_bloc_selectedThis file contain all the sequences aligned after bloc removal for each trees.sequences_aligned_and_bloc_selected.7ztrees
DOI: 10.5061/dryad.69bb2
title: Data from: Probabilistic distances between trees

description: Most existing measures of distance between phylogenetic trees are based on
 the geometry or topology of the trees. Instead, we consider distance
 measures which are based on the underlying probability distributions on
 genetic sequence data induced by trees. Monte Carlo schemes are necessary
 to calculate these distances approximately, and we describe efficient
 sampling procedures. Key features of the distances are the ability to
 include substitution model parameters and to handle trees with different
 taxon sets in a principled way. We demonstrate some of the properties of
 these new distance measures and compare them to existing distances, in
 particular by applying multidimensional scaling to data sets previously
 reported as containing phylogenetic islands.
description: AppendixOnline-only appendixappendix.pdfSoftware and data setsprobabilistic_distances.tar.gz