cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9g54r
title: Data from: Reconstruction of the cortical maps of the Tasmanian tiger and comparison to the Tasmanian devil

description: The last known Tasmanian tiger (Thylacinus cynocephalus)–aka the
 thylacine–died in 1936. Because its natural behavior was never
 scientifically documented, we are left to infer aspects of its behavior
 from museum specimens and historical recollections of bushmen. Recent
 advances in brain imaging have made it possible to scan postmortem
 specimens of a wide range of animals, even more than a decade old. Any
 thylacine brain, however, would be more than 100 years old. Here, we show
 that it is possible to reconstruct white matter tracts in two thylacine
 brains. For functional interpretation, we compare to the white matter
 reconstructions of the brains of two Tasmanian devils (Sarcophilus
 harrisii). We reconstructed the cortical projection zones of the basal
 ganglia and major thalamic nuclei. The basal ganglia reconstruction showed
 a more modularized pattern in the cortex of the thylacine, while the devil
 cortex was dominated by the putamen. Similarly, the thalamic projections
 had a more orderly topography in the thylacine than the devil. These
 results are consistent with theories of brain evolution suggesting that
 larger brains are more modularized. Functionally, the thylacine’s brain
 may have had relatively more cortex devoted to planning and
 decision-making, which would be consistent with a predatory ecological
 niche versus the scavenging niche of the devil.
description: thylacine_smithsonianStructural images and outputs from BEDPOSTX and DTIFIT for the Smithsonian thylacine brain (USNM 125345).thylacine_sydneyStructural images and outputs of BEDPOSTX and DTIFIT for the Australian Museum thylacine brain (M18411). Contains very high resolution structural (0.1 x 0.1 x 0.2 mm).devil_smithsonianStructural images and outputs from BEDPOSTX and DTIFIT for the Smithsonian Tasmanian devil brain (USNM 142598).devil_STDPStructural images and outputs from BEDPOSTX and DTIFIT from Tasmanian devil brain (provided by the Save the Devil Project).
DOI: 10.5061/dryad.2q8p6
title: Data from: Rapid genetic and ecological differentiation during the northern range expansion of the venomous yellow sac spider Cheiracanthium punctorium in Europe

description: Although poleward range expansions are commonly attributed to global
 change, a complex interaction of ecological and evolutionary factors might
 contribute to expansion success. Here, we study the expansion of the
 yellow sac spider Cheiracanthium punctorium, a medically important species
 in Central Europe. Using microsatellite markers and DNA sequences,
 morphological and climate niche analyses, we identify factors associated
 with the spider’s expansion success. Our results indicate that the
 species’ initial expansion has been triggered by environmental change and
 preadaptation in the source populations. However, despite extensive gene
 flow, expanding populations maintain genetic and morphological
 differentiation from native ones, which is correlated with climatic niche
 differences. Moreover, expanding spiders might have temporarily escaped an
 eggsac parasite that causes high mortality in the native range. Hence, our
 results paint a complex picture of diverse factors associated with
 expansion success. We speculate that expanding populations might be
 capable of adapting to novel ecological conditions in Northern Europe.
 This could allow a substantial range expansion, much farther than by
 environmental change alone. Our distribution model predicts that the
 spider will soon massively spread over most of Northern Europe, bringing
 along considerable health concerns.
description: 28SrDNA_AlignmentCOI_AlignmentMicrosatellite_dataMicrosatellite_primersMorphological_measurementsSampling_sitesDistributional_recordsRecords for the distribution modellingCheiracanthium_punctorium_assemblyLow coverage genome assembly
DOI: 10.5061/dryad.jc402
title: Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes

description: Gene duplication is important in evolution, because it provides new raw
 material for evolutionary adaptations. Several existing hypotheses about
 the causes of duplicate retention and diversification differ in their
 emphasis on gene dosage, sub-functionalization, and neo-functionalization.
 Little experimental data exists on the relative importance of gene
 expression changes and changes in coding regions for the evolution of
 duplicate genes. Furthermore, we do not know how strongly the environment
 could affect this importance. To address these questions, we performed
 evolution experiments with the TEM-1 beta lactamase gene in E. coli to
 study the initial stages of duplicate gene evolution in the laboratory. We
 mimicked tandem duplication by inserting two copies of the TEM-1 gene on
 the same plasmid. We then subjected these copies to repeated cycles of
 mutagenesis and selection in various environments that contained
 antibiotics in different combinations and concentrations. Our experiments
 showed that gene dosage is the most important factor in the initial stages
 of duplicate gene evolution, and overshadows the importance of point
 mutations in the coding region.
description: Evolution_sequencing_dataThis file contains 454 amplicon sequencing data for the ancestral strains and the evolved lines (EvoS and EvoD lines). The file includes raw sequencing data as well as alignment files.
DOI: 10.5061/dryad.0mv56
title: Data from: "De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

description: Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to
 the European montane/alpine zone (Bächli 2008). Mountain biodiversity is
 considered highly vulnerable to ongoing climate warming (IPCC 2013), and
 organisms at high altitudes have only limited possibility to shift to
 cooler habitats at elevations above (Pertoldi & Bach 2007). For
 such species, rapid evolution may offer a solution for long-term survival.
 We are establishing D. nigrosparsa as a model system to test the extent
 and tempo of adaptive evolution under thermal stress in the laboratory. In
 this study, we used Illumina high-throughput sequencing to assemble the
 species’ transcriptome using the pooled mRNA from 22 developmental and
 physiological stages.
description: Dnig trinity
 contigsDnig annotated
 unigenesDnig annotated
 proteinsDnig annotated
 transcripts v2ScriptsShellscripts used in the bioinformatic pipeline
DOI: 10.5061/dryad.6939c
title: Data from: Integrating continuous stocks and flows into state-and-transition simulation models of landscape change

description: 1.State-and-transition simulation models (STSMs) provide a general
 framework for forecasting landscape dynamics, including projections of
 both vegetation and land-use/land-cover (LULC) change. The STSM method
 divides a landscape into spatially-referenced cells and then simulates the
 state of each cell forward in time, as a discrete-time stochastic process
 using a Monte Carlo approach, in response to any number of possible
 transitions. A current limitation of the STSM method, however, is that all
 of the state variables must be discrete. 2.Here we present a new approach
 for extending a STSM, in order to account for continuous state variables,
 called a state-and-transition simulation model with stocks and flows
 (STSM-SF). The STSM-SF method allows for any number of continuous stocks
 to be defined for every spatial cell in the STSM, along with a suite of
 continuous flows specifying the rates at which stock levels change over
 time. The change in the level of each stock is then simulated forward in
 time, for each spatial cell, as a discrete-time stochastic process. The
 method differs from the traditional systems dynamics approach to
 stock-flow modelling in that the stocks and flows can be
 spatially-explicit, and the flows can be expressed as a function of the
 STSM states and transitions. 3.We demonstrate the STSM-SF method by
 integrating a spatially-explicit carbon (C) budget model with a STSM of
 LULC change for the state of Hawai'i, USA. In this example,
 continuous stocks are pools of terrestrial C, while the flows are the
 possible fluxes of C between these pools. Importantly, several of these C
 fluxes are triggered by corresponding LULC transitions in the STSM. Model
 outputs include changes in the spatial and temporal distribution of C
 pools and fluxes across the landscape in response to projected future
 changes in LULC over the next 50 years. 4.The new STSM-SF method allows
 both discrete and continuous state variables to be integrated into a STSM,
 including interactions between them. With the addition of stocks and
 flows, STSMs provide a conceptually simple yet powerful approach for
 characterizing uncertainties in projections of a wide range of questions
 regarding landscape change.
description: Case study files for
 ST-Sim softwareAs outlined in Appendix
 S1, this file contains all of the files required to run and view the
 results of the paper's simulations using the ST-Sim
 softwarestsmsf-case-study-2017-09-08.zip
DOI: 10.5061/dryad.p58c0
title: Data from: Body shape diversity in Triassic‒Early Cretaceous neopterygian fishes: sustained holostean disparity and predominantly gradual increases in teleost phenotypic variety

description: Comprising Holostei and Teleostei, the ~32,000 species of neopterygian
 fishes are anatomically disparate and represent the dominant group of
 aquatic vertebrates today. However, the pattern by which teleosts rose to
 represent almost all of this diversity, while their holostean sister group
 dwindled to 8 extant species and two broad morphologies, is poorly
 constrained. A geometric morphometric approach was taken to generate a
 morphospace from over 400 fossil taxa, representing almost all articulated
 neopterygian taxa known from the first 150 million years—roughly 60%—of
 history (Triassic‒Early Cretaceous). Patterns of morphospace occupancy and
 disparity are examined in order to: assess evidence for a phenotypically
 'dominant' holostean phase; evaluate whether expansions in
 teleost phenotypic variety are predominantly abrupt or gradual, including
 assessment of whether apomorphy-defined teleosts are as morphologically
 conservative as typically assumed; compare diversification in crown and
 stem teleosts. The systematic affinities of dapediiforms and
 pycnodontiforms, two extinct neopterygian clades of uncertain phylogenetic
 placement, significantly impact patterns of morphological diversification.
 For instance, alternative placements dictate whether or not holosteans
 possessed statistically higher disparity than teleosts in the Late
 Triassic and Jurassic. Despite this ambiguity, all scenarios agree that
 holosteans do not exhibit a decline in disparity during the Early
 Triassic‒Early Cretaceous interval, but instead maintain their
 Toarcian‒Callovian variety until the end of the Early Cretaceous without
 substantial further expansions. After a conservative Induan‒Carnian phase,
 teleosts colonize (and persistently occupy) novel regions of morphospace
 in a predominantly gradual manner until the Hauterivian, after which
 expansions are rare. Furthermore, apomorphy-defined teleosts possess
 greater phenotypic variety than typically assumed. Comparison of crown and
 stem teleost partial disparity indicates that, despite substantial
 expansion in crown teleosts between the Late Jurassic and earliest
 Cretaceous, stem teleosts remained important long-term contributors to
 overall teleost disparity during this time.
description: SI Figures
 S1-S17All 17 SI figures with
 captions.SI.Figures_S1-S17.pdfSI tables S1-S7All 7 SI tables with captions.SI.tables.1-7.xlsxAnalysis.filesInput and output files for analyses with R code.
DOI: 10.5061/dryad.510tp
title: Data from: Taking the discovery approach in integrative taxonomy: decrypting a complex of narrow-endemic Alpine harvestmen (Opiliones: Phalangiidae: Megabunus)

description: Species delimitation is fundamental for biological studies, yet precise
 delimitation is not an easy task, and every involved approach has an
 inherent failure rate. Integrative taxonomy, a method that merges multiple
 lines of evidence, can profoundly contribute to reliable alpha taxonomy
 and shed light on the processes behind speciation. In this study, we
 explored and validated species limits in a group of closely related
 Megabunus harvestmen (Eupnoi, Phalangiidae) endemic to the European Alps.
 Without a priori species hypotheses, we used multiple sources of
 inference, including mitochondrial and multilocus nuclear DNA,
 morphometrics, and chemistry. The results of these discovery approaches
 revealed morphological crypsis and multiple new species within two of the
 five hitherto known species. Based on our analyses, we discussed the most
 plausible evolutionary scenarios, invoked the most reasonable species
 hypotheses, and validated the new species limits. Building upon the
 achieved rigour, three new species, M. cryptobergomas Muster &
 Wachter sp. nov., M. coelodonta Muster & Steiner sp. nov., and M.
 lentipes Muster & Komposch sp. nov., are formally described. In
 addition, we provide a dichotomous morphological key to the Megabunus
 species of the Alps. Our work demonstrates the suitability of integrative,
 discovery-based approaches in combination with validation approaches to
 precisely characterise species and enabled us to implement nomenclatural
 consequences for this genus.
description: nuDNA Meg14 fasta
 fileContains fasta sequences
 of anonymous locus Meg14 for all individuals used in this
 studyMeg14.fastanuDNA Meg15 fasta fileContains fasta sequences of anonymous locus Meg15 for all individuals used in this studyMeg15.fastanuDNA Meg52 fasta fileContains fasta sequences of anonymous locus Meg52 for all individuals used in this studyMeg52.fastanuDNA Meg60 fasta fileContains fasta sequences of anonymous locus Meg60 for all individuals used in this studyMeg60.fastanuDNA Meg77 fasta fileContains fasta sequences of anonymous locus Meg77 for all individuals used in this studyMeg77.fastanuDNA Meg119 fasta fileContains fasta sequences of anonymous locus Meg119 for all individuals used in this studyMeg119.fastaTableS6 - CHC profilesContains a table with individual cuticular profiles for all individuals used in this studyTableS6.xlsTableS7 - Morphometric charactersContains a table with measurements of twelve characters of the legs for all individuals used in this studyTableS7.xlsDigital_Images_Cephalothorax_dorsal_MegabunusContains digital images of the cephalothorax in dorsal view for all individuals used in this study16srRNA fasta fileContains fasta sequences of mitochondrial 16SrRNA for all individuals used in this study16s.fas
DOI: 10.5061/dryad.mj8m0
title: Data from: Reptile embryos lack the opportunity to thermoregulate by moving within the egg

description: Thermal taxis by egg-bound embryos has been observed in multiple reptiles
 and might allow embryos to behaviorally thermoregulate. Because
 temperature affects development, such thermoregulation could allow embryos
 to control their fate far more than historically assumed. We assessed the
 opportunity for embryos to behaviorally thermoregulate in nature by
 examining thermal gradients within natural nests and eggs of the common
 snapping turtle (Chelydra serpentina, a species that displays embryonic
 thermal taxis) and, more generally, by simulating thermal gradients within
 nests across a range of nest depths, egg sizes, and soil types. We
 observed little spatial thermal variation within C. serpentina nests, and
 thermal gradients were poorly transferred to eggs. Furthermore, thermal
 gradients sufficiently large and constant for behavioral thermoregulation
 were not predicted to occur in our simulations. Gradients of
 biologically-relevant magnitude have limited global occurrence, and
 reverse direction twice daily when they do exist, which is substantially
 faster than embryos can shift position within the egg. Our results imply
 that reptile embryos will rarely, if ever, have the opportunity to
 behaviorally thermoregulate by moving within the egg. We suggest that
 embryonic thermal taxis instead represents a play behavior, which may be
 adaptive or selectively neutral, and results from the mechanisms for
 behavioral thermoregulation in free-living stages "coming
 online" prior to hatching.
description: Nest temperature
 dataData provide
 temperatures at 4 depths within natural Chelydra serpentina nests, from
 IL, USANestTemperatureData.csvExternal egg temperaturesData are temperatures on the shell surface of Chelydra serpentina eggs exposed to large and small thermal gradient treatments within the laboratory.ExternalTemps.csvInternal egg temperaturesData are temperatures within live eggs exposed to either a small or large thermal gradient in the laboratory.InternalEggTempData.csvSoilSimulation_OutputSimulated soil temperature data using the Campbell and Norman (1998) model. Data used to assess the potential for embryos to experience biologically-relevant thermal gradients. File is too large to be opened in MS Excel.
DOI: 10.5061/dryad.15423
title: Data from: Habitat suitability and the constraints of migration in New World warblers

description: Identifying the factors that influence geographic range limits can
 illustrate the various ecological, physiological, and evolutionary
 constraints imposed on a species. The range limits of migratory birds are
 particularly challenging to study as they occur in disjunct regions at
 different times of the year, which can impose different constraints.
 Travel between breeding and wintering regions poses a significant
 energetic and navigational challenge to birds, although it is not clear
 how these movements influence breeding dispersal and range expansion. Here
 I ask whether the possible costs of migration limit the breeding ranges of
 wood warblers, a group of birds with an extensive history of ecological
 and evolutionary studies. I used occurrence records for multiple wood
 warbler species, breeding primarily in the boreal forest of North America,
 to generate environmental niche models. I tested for over-prediction of
 habitat suitability into the western boreal forest, where most these
 species do not have occurrence records but where there is presumably
 suitable habitat. I found that these vagile taxa, primarily found east of
 the Rocky Mountains, also have predicted habitat suitability that extends
 into the north and west, where they have little to no occurrence records.
 I discuss several possible explanations for this discordance. In
 particular, the patterns are consistent with the costs of a long-distance
 migration limiting the benefits of range expansion, as migration may
 become too onerous as the distance between breeding and wintering areas
 increases. These results speak to the process of niche filling more
 generally and call attention to an under-appreciated explanation for why
 migratory species may not fully occupy their fundamental niche.
description: MAXENT Output ASCII
 filesZip file that contains
 MAXENT output files in ASCII format. Full details for the 17 warbler
 species can be found in the text.warbler_ascii.zip
DOI: 10.5061/dryad.55nb0
title: Data from: Bacterial characterization of Beijing drinking water by flow cytometry and MiSeq sequencing of the 16S rRNA gene

description: Flow cytometry (FCM) and 16S rRNA gene sequencing data are commonly used
 to monitor and characterize microbial differences in drinking water
 distribution systems. In this study, to assess microbial differences in
 drinking water distribution systems, 12 water samples from different
 sources water (groundwater, GW; surface water, SW) were analyzed by FCM,
 heterotrophic plate count (HPC), and 16S rRNA gene sequencing. FCM intact
 cell concentrations varied from 2.2 × 103 cells/mL to 1.6 × 104 cells/mL
 in the network. Characteristics of each water sample were also observed by
 FCM fluorescence fingerprint analysis. 16S rRNA gene sequencing showed
 that Proteobacteria (76.9–42.3%) or Cyanobacteria (42.0–3.1%) was most
 abundant among samples. Proteobacteria were abundant in samples containing
 chlorine, indicating resistance to disinfection. Interestingly,
 Mycobacterium, Corynebacterium, and Pseudomonas, were detected in drinking
 water distribution systems. There was no evidence that these
 microorganisms represented a health concern through water consumption by
 the general population. However, they provided a health risk for special
 crowd, such as the elderly or infants, patients with burns and
 immune-compromised people exposed by drinking. The combined use of FCM to
 detect total bacteria concentrations and sequencing to determine the
 relative abundance of pathogenic bacteria resulted in the quantitative
 evaluation of drinking water distribution systems. Knowledge regarding the
 concentration of opportunistic pathogenic bacteria will be particularly
 useful for epidemiological studies.
description: liu ting ting-sequencing
 RawData
DOI: 10.5061/dryad.3t5g3
title: Data from: Effective size of density-dependent populations in fluctuating environments

description: Reliable estimates of effective population size Ne are of central
 importance in population genetics and evolutionary biology. For
 populations that fluctuate in size, harmonic mean population size is
 commonly used as a proxy for (multi-) generational effective size. This
 assumes no effects of density dependence on the ratio between effective
 and actual population size, which limits its potential application. Here
 we introduce density dependence on vital rates in a demographic model of
 variance effective size. We derive an expression for the ratio Ne/N in a
 density regulated population in a fluctuating environment. We show by
 simulations that yearly genetic drift is accurately predicted by our
 model, and not proportional to 1/(2N) as assumed by the harmonic mean
 model, where N is the total population size of mature individuals. We find
 a negative relationship between Ne/N and N. For a given N, the ratio
 depends on variance in reproductive success and the degree of resource
 limitation acting on the population growth rate. Finally, our model
 indicate that environmental stochasticity may affect Ne/N not only through
 fluctuations in N, but also for a given N at a given time. Our results
 show that estimates of effective population size must include effects of
 density dependence and environmental stochasticity.
description: simulated data on
 density dependent populations and genetic drift and accompanying
 codesIncludes "raw"
 datafiles based on simulations used to estimate effective population size
 of monoecious populations in average environment and in fluctuating
 environments. Also includes datafiles based on simulations used to
 estimate LRS and generation time with respect to the population size at
 birth N0 (used in Table 2 in article). The codes used to generate the
 simulated data are also attached.Data.zip