cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3526q
title: Data from: Mice infected with low-virulence strains of Toxoplasma gondii lose their innate aversion to cat urine, even after extensive parasite clearance

description: Toxoplasma gondii chronic infection in rodent secondary hosts has been
 reported to lead to a loss of innate, hard-wired fear toward cats, its
 primary host. However the generality of this response across T. gondii
 strains and the underlying mechanism for this pathogen-mediated behavioral
 change remain unknown. To begin exploring these questions, we evaluated
 the effects of infection with two previously uninvestigated isolates from
 the three major North American clonal lineages of T. gondii, Type III and
 an attenuated strain of Type I. Using an hour-long open field activity
 assay optimized for this purpose, we measured mouse aversion toward
 predator and non-predator urines. We show that loss of innate aversion of
 cat urine is a general trait caused by infection with any of the three
 major clonal lineages of parasite. Surprisingly, we found that infection
 with the attenuated Type I parasite results in sustained loss of aversion
 at times post infection when neither parasite nor ongoing brain
 inflammation were detectable. This suggests that T. gondii-mediated
 interruption of mouse innate aversion toward cat urine may occur during
 early acute infection in a permanent manner, not requiring persistence of
 parasite cysts or continuing brain inflammation.
description: Motor Monitor Data from
 Kinder Scientific reduced files - 1 min intervalsReduced data for 3
 weeks, 2 months, and 4 months post infection with Type I or Type III
 parasites.MotorMonitor_Balbc_Coh3.xlsx
DOI: 10.5061/dryad.b854d
title: Data from: Diachronous increase in early Cambrian ichnofossil size and benthic faunal activity in different climatic regions

description: In order to clarify the pattern of diversification and processes of
 biological activity during the Cambrian radiation, ichnofossils were
 comparatively studied in the early Cambrian sections of Newfoundland,
 South China and western Mongolia. Special attention was paid to size
 distributions of the most common ichnogenus, Planolites, and the densities
 of all the observed ichnofossils that preserve animal activity as
 expressed by bedding plane bioturbation indices (BPBI). From the Fortune
 Head section in Newfoundland, a clear size increase in the ichnogenus
 Planolites is confirmed from the Treptichnus pedum Zone to the overlying
 Rusophycus avalonensis Zone. The BPBI also shows much stronger biological
 activity in the R. avalonensis Zone than in the T. pedum Zone. In
 Meishucun, South China and Gobi-Altai, Mongolia, however, a variety of
 Planolites sizes had already appeared in the T. pedum Zone, and the
 BPBI's on some bedding surfaces of the T. pedum Zone are already
 comparable to those in the R. avalonensis Zone in Newfoundland. In the
 earliest Cambrian, diversification and increase in the biological activity
 of the benthic fauna were diachronous in the wide geographic scale,
 starting earlier at lower latitudes (South China and western Mongolia)
 than at higher latitudes (Newfoundland), reflecting differences in the
 onset of Cambrian benthic animal activity under different climatic
 conditions.
description: Supplemental figure
 1SUPPLEMENTAL DATA
 1—Columnar section of the Treptichnus pedum Zone of the Chapel Island
 Formation in Fortune Head, Newfoundland.Supplemental figure
 2SUPPLEMENTAL DATA
 2—Columnar section of the Rusophycus avalonensis Zone of the Chapel Island
 Formation in Fortune Head, Newfoundland.Supplemental figure
 3SUPPLEMENTAL DATA
 3—Columnar section of the uppermost Dengying and Zhujiaqing formations in
 Meishucun, Yunnan.Supplemental figure
 4SUPPLEMENTAL DATA
 4—Columnar section of the Tsagaan Oloom and Bayan Gol formations in Bayan
 Gol gorge, Gobi-Altai.Supplemental figure
 CaptionsSupplemental figure
 captions.
DOI: 10.5061/dryad.1d60p
title: Data from: Predicting local and non-local effects of resources on animal space use using a mechanistic step-selection model

description: 1. Predicting space use patterns of animals from their interactions with
 the environment is fundamental for understanding the effect of habitat
 changes on ecosystem functioning. Recent attempts to address this problem
 have sought to unify resource selection analysis, where animal space use
 is derived from available habitat quality, and mechanistic movement
 models, where detailed movement processes of an animal are used to predict
 its emergent utilisation distribution. Such models bias the animal's
 movement towards patches that are easily available and resource-rich, and
 the result is a predicted probability density at a given position being a
 function of the habitat quality at that position. However, in reality, the
 probability that an animal will use a patch of the terrain tends to be a
 function of the resource quality in both that patch and the surrounding
 habitat. 2. We propose a mechanistic model where this non-local effect of
 resources naturally emerges from the local movement processes, by taking
 into account the relative utility of both the habitat where the animal
 currently resides and that of where it is moving. We give statistical
 techniques to parametrize the model from location data, and demonstrate
 application of these techniques to GPS location data of caribou (Rangifer
 tarandus) in Newfoundland. 3. Steady-state animal probability
 distributions arising from the model have complex patterns that cannot be
 expressed simply as a function of the local quality of the habitat. In
 particular, large areas of good habitat are used more intensively than
 smaller patches of equal quality habitat, whereas isolated patches are
 used less frequently. Both of these are real aspects of animal space use
 missing from previous mechanistic resource-selection models. 4. Whilst we
 focus on habitats in this paper, our modelling framework can be readily
 used with any environmental covariates, and therefore represents a
 unification of mechanistic modelling and step-selection approaches to
 understanding animal space use.
description: nc_pottsetal_online_dataData on distances between successive locations of Caribou, the habitats at the start and end of the steps, and the probabilities that we would expect each step to end in each habitat if there is no selection.
DOI: 10.5061/dryad.4dv78
title: Data from: Predator perception of Batesian mimicry and conspicuousness in a salamander

description: In Batesian mimicry a palatable mimic deceives predators by resembling an
 unpalatable model. The evolution of Batesian mimicry relies on the visual
 capabilities of the potential predators, as prey detection provides the
 selective force driving evolutionary change. We compared the visual
 capabilities of several potential predators to test predictions stemming
 from the hypothesis of Batesian mimicry between two salamanders: the model
 species Notophthalmus viridescens, and polymorphic mimic, Plethodon
 cinereus. First, we found mimicry to be restricted to coloration, but not
 brightness. Second, only bird predators appeared able to discriminate
 between the colors of models and non-mimic P. cinereus. Third, estimates
 of salamander conspicuousness were background-dependent, corresponding to
 predictions only for backgrounds against which salamanders are most
 active. These results support the hypothesis that birds influence the
 evolution of Batesian mimicry in P. cinereus, as they are the only group
 examined capable of differentiating N. viridescens and non-mimetic P.
 cinereus. Additionally, patterns of conspicuousness suggest that selection
 from predators may drive the evolution of conspicuousness in this system.
 This study confirms the expectation that the visual abilities of predators
 may influence the evolution of Batesian mimicry, but the role of
 conspicuousness may be more complex than previously thought.
description: VisModelsMimicryDataThis dataset includes the reflectance spectra for all salamanders in the study, as well as the background spectra used in analyses.
DOI: 10.5061/dryad.h97pk
title: Data from: Species radiation by niche shifts in New Zealand’s rockcresses (Pachycladon, Brassicaceae)

description: Adaptive radiations such as the Darwin finches in the Galapagos or the
 cichlid fishes from the Eastern African Great Lakes have been a constant
 source of inspiration for biologists and a stimulus for evolutionary
 thinking. A central concept behind adaptive radiation is that of evolution
 by niche shifts, or ecological speciation. Evidence for adaptive
 radiations generally requires a strong correlation between phenotypic
 traits and the environment. But adaptive traits are often cryptic, hence
 making this phenotype-environment approach difficult to implement. Here we
 propose a procedure for detecting adaptive radiation that focuses on
 species’ ecological niche comparisons. It evaluates whether past
 ecological disparity in a group fits better a neutral Brownian motion
 model of ecological divergence or a niche shift model. We have evaluated
 this approach on New Zealand rockcresses (Pachycladon) that recently
 radiated in the New Zealand Alps. We show that the pattern of ecological
 divergence rejects the neutral model and is consistent with that of a
 niche shift model. Our approach to detect adaptive radiation has the
 advantage over alternative approaches that it focuses on ecological
 niches, a key concept behind adaptive radiation. It also provides a way to
 evaluate the importance of ecological speciation in adaptive radiations
 and will have general application in evolutionary studies. In the case of
 Pachycladon, the high estimated diversification rate, the distinctive
 ecological niches of species, and the evidence for ecological speciation
 suggest a remarkable example of adaptive radiation.
description: R
 scriptsR scripts to perform the
 analyses performed in the paper.Joly&al_SystBiol_R_scripts.R*Beast analysis xml filexml file used to perform the species tree analysis.*Beast_analysis_ConstantPopSize.xmlbpp Species Delim Control Filecontrol file used to perform the BP&P species delimitation analysis.bpp_SpeciesDelimControlFile.ctlSupplementary figuresSupplementary figures 1, 2, and 3.Supp_figures.pdfSupplementary table 1Table S1TableS1.docxSupplementary table 2Table S2TableS2.docxSupplementary table 3Table S3TableS3.docx
DOI: 10.15468/dl.f4rk55
title: Occurrence Download

description: A dataset listing the 94 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "GadmGid is COL.15_2",
 "IucnRedListCategory is one of (EN, CR, VU)",
 "PublishingOrg is 2a7e3080-28a9-11dd-97cd-b8a03c50a862"
 ]
}

 The dataset's 94 records were derived from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001586-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3074s
title: Data from: Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions

description: Multigene families have provided opportunities for evolutionary biologists
 to assess molecular evolution processes and phylogenetic reconstructions
 at deep and shallow systematic levels. However, the use of these markers
 is not free of technical and analytical challenges. Many evolutionary
 studies that used the nuclear 5S rDNA gene family rarely used contiguous
 5S coding sequences due to the routine use of head-to-tail PCR primers
 that are anchored to the coding region. Moreover, the 5S coding sequences
 have been concatenated with independent, adjacent gene units in many
 studies, creating simulated chimeric genes as the raw data for
 evolutionary analysis. This practice is based on the tacitly assumed, but
 rarely tested, hypothesis that strict intra-locus concerted evolution
 processes are operating in 5S rDNA genes, without any empirical evidence
 as to whether it holds for the recovered data. The potential pitfalls of
 analysing the patterns of molecular evolution and reconstructing
 phylogenies based on these chimeric genes have not been assessed to date.
 Here, we compared the sequence integrity and phylogenetic behaviour of
 entire versus concatenated 5S coding regions from a real data set obtained
 from closely related plant species (Medicago, Fabaceae). Our results
 suggest that within arrays sequence homogenization is partially operating
 in the 5S coding region, which is traditionally assumed to be highly
 conserved. Consequently, concatenating 5S genes increases haplotype
 diversity, generating novel chimeric genotypes that most likely do not
 exist within the genome. In addition, the patterns of gene evolution are
 distorted, leading to incorrect haplotype relationships in some
 evolutionary reconstructions.
description: Online supplementary
 Figure 1Online Supplementary
 Figure 1. Concatenation of the 26 haplotypes found in the 16 multimeric
 clones analyzed in this paper. Note that chimeric types appear shorter
 than interior non-chimeric types. As explained in methods, chimerics are
 constructed using the closest complementary part of the interior 5S gene
 but this part is not represented in order to clarify the
 scheme.O_S_Figure_1.pdfOnline Supplementary Figure 2Online Supplementary Figure 2. Secondary structures of the predicted 5S rRNA transcripts for 26 Medicago haplotypes. Variable positions differing from the consensus sequence (haplotype 1) are identified with arrow heads.O_S_Figure_2.pdf
DOI: 10.5061/dryad.5cs38
title: Data from: Transcriptional responses in a Drosophila defensive symbiosis

description: Inherited symbionts are ubiquitous in insects and can have important
 consequences for the fitness of their hosts. Many inherited symbionts
 defend their hosts against parasites or other natural enemies; however,
 the means by which most symbionts confer protection is virtually unknown.
 We examine the mechanisms of defence in a recently discovered case of
 symbiont-mediated protection, where the bacterial symbiont Spiroplasma
 defends the fly Drosophila neotestacea from a virulent nematode parasite,
 Howardula aoronymphium. Using quantitative PCR of Spiroplasma infection
 intensities and whole transcriptome sequencing, we attempt to distinguish
 between the following modes of defence: symbiont–parasite competition,
 host immune priming and the production of toxic factors by Spiroplasma.
 Our findings do not support a model of exploitative competition between
 Howardula and Spiroplasma to mediate defence, nor do we find strong
 support for host immune priming during Spiroplasma infection.
 Interestingly, we recovered sequence for putative toxins encoded by
 Spiroplasma, including a novel putative ribosome-inactivating protein,
 transcripts of which are up-regulated in response to nematode exposure.
 Protection via the production of toxins may be a widely used and important
 mechanism in heritable defensive symbioses in insects.
description: Hamilton_etal_DryadData2013Compressed archive of data files and transcriptome assembly used in analysis.Hamilton_etal_Dryad.zip
DOI: 10.5061/dryad.6575f
title: Data from: Advancing population ecology with integral projection models: a practical guide

description: Integral Projection Models (IPMs) use information on how an
 individual's state influences its vital rates - survival, growth and
 reproduction - to make population projections. IPMs are constructed from
 regression models predicting vital rates from state variables (e.g., size
 or age) and covariates (e.g., environment). By combining regressions of
 vital rates, an IPM provides mechanistic insight into emergent ecological
 patterns such as population dynamics, species geographic distributions, or
 life history strategies. Here, we review important resources for building
 IPMs and provide a comprehensive guide, with extensive R code, for their
 construction. IPMs can be applied to any stage-structured population; here
 we illustrate IPMs for a series of plant life histories of increasing
 complexity and biological realism, highlighting the utility of various
 regression methods for capturing biological patterns. We also present case
 studies illustrating how IPMs can be used to predict species’ geographic
 distributions and life history strategies. IPMs can represent a wide range
 of life histories at any desired level of biological detail. Much of the
 strength of IPMs lies in the strength of regression models. Many
 subtleties arise when scaling from vital rate regressions to
 population-level patterns, so we provide a set of diagnostics and
 guidelines to ensure that models are biologically plausible. Moreover,
 IPMs can exploit a large existing suite of analytical tools developed for
 Matrix Projection Models.
description: Appendix_A_Simple_dataSimulated data to be used with tutorials in Appendix A.Tree_dataData to be used with tutorials in Appendix D.cleanedClarkClarkData to be used with tutorials in Appendix E.ActaeaRegDatSimulated data to be used with tutorials in Appendix F.
DOI: 10.5061/dryad.mq8n5
title: Data from: Performance of individual vs group sampling for inferring dispersal under isolation by distance

description: Models of isolation-by-distance formalize the effects of genetic drift and
 gene flow in a spatial context where gene dispersal is spatially limited.
 These models have been used to show that, at an appropriate spatial scale,
 dispersal parameters can be inferred from the regression of genetic
 differentiation against geographic distance between sampling locations.
 This approach is compelling because it is relatively simple and robust,
 and has rather low sampling requirements. In continuous populations,
 dispersal can be inferred from isolation-by-distance patterns using either
 individuals or groups as sampling units. Intrigued by empirical findings
 where individual samples seemed to provide more power, here we used
 simulations to compare the performances of the two methods in a range of
 situations with different dispersal distributions. We found that sampling
 individuals provides more power in a range of dispersal conditions that is
 narrow but fits many realistic situations. These situations were
 characterized not only by the general steepness of isolation-by-distance
 but also by the intrinsic shape of the dispersal kernel. The performances
 of the two approaches are otherwise similar, suggesting that the choice of
 a sampling unit is globally less important than other settings such as a
 study's spatial scale.
description: READMEDescription of archived
 files.SimulsDetails of simulation
 scenariosIBD_SettingsParameter files for simulations performed with software IBDSim (Leblois et al. 2009)Genepop_Group_SettingsParameter file for analysing simulation outputs in software Genepop (Rousset 2008)Genepop_Ind_SettingsParameter file for analyzing simulation outputs in software Genepop (Rousset 2008) at the individual levelGroup_ResultsCollection of useful statistics (used for the analyses presented in the paper) from all simulations and genepop output at the group levelInd_ResultsCollection of useful statistics (used for the analyses presented in the paper) from all simulations and genepop output at the individual level
DOI: 10.5061/dryad.96k0t
title: Data from: Taphonomy of the Ediacaran fossil Pteridinium simplex preserved three-dimensionally in mass flow deposits, Nama Group, Namibia

description: Ediacara-type fossils are found in a diverse array of preservational
 styles, implying that multiple taphonomic mechanisms might have been
 responsible for their preservational expression. For many Ediacara
 fossils, the “death mask” model has been invoked as the primary taphonomic
 pathway. The key to this preservational regime is the replication or
 sealing of sediments around the degrading organisms by microbially induced
 precipitation of authigenic pyrite, leading toward fossil preservation
 along bedding planes. Nama-style preservation, on the other hand, captures
 Ediacaran organisms as molds and three-dimensional casts within
 coarse-grained mass flow beds, and has been previously regarded as showing
 little or no evidence of a microbial preservational influence. To further
 understand these two seemingly distinct taphonomic pathways, we
 investigated the three-dimensionally preserved Ediacaran fossil
 Pteridinium simplex from mass flow deposits of the upper Kliphoek Member,
 Dabis Formation, Kuibis Subgroup, southern Namibia. Our analysis, using a
 combination of petrographic and micro-analytical methods, shows that
 Pteridinium simplex vanes are replicated with minor pyrite, but are most
 often represented by open voids that can be filled with secondary
 carbonate material; clay minerals are also found in association with the
 vanes, but their origin remains unresolved. The scarcity of pyrite and the
 development of voids are likely related to oxidative weathering and it is
 possible that microbial activities and authigenic pyrite may have
 contributed to the preservation of Pteridinium simplex; however, any
 microbes growing on P. simplex vanes within mass flow deposits were
 unlikely to have formed thick mats as envisioned in the death mask model.
 Differential weathering of replicating minerals and precipitation of
 secondary minerals greatly facilitate fossil collection and morphological
 characterization by allowing Pteridinium simplex vanes to be parted from
 the massive hosting sandstone.
description: SUPPLEMENTAL DATA FIGURE
 1BSE-Z images showing
 locations of EDS point analyses on P. simplex vanes and matrix. Data are
 shown in Table 1. Scale bar in 1=500 µm, in 2=100 µm, in 3 and 4=1 mm, in
 5 and 6=400 µm, and in 7 and 8=100 µm.PteriTaphFigSD_Dryad-01.jpg