cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c5g25
title: Data from: Hurdiid radiodontans from the middle Cambrian (Series 3) of Utah

description: Radiodontan body elements, some belonging to Peytoia and Hurdia and some
 unassigned, have been reported from the Langston Formation (Spence Shale
 Member), Wheeler Formation, and Marjum Formation of the middle Cambrian
 (Series 3) of Utah. These identifications are reassessed in light of
 recent work on the morphology of the radiodontan Hurdia. New specimens of
 Hurdia are identified from the Spence Shale, representing mouthparts (oral
 cones), cephalic carapace H-elements, frontal appendages, and a single
 isolated swimming flap. The shape of the H-elements allows H. victoria
 Walcott, 1912 to be identified from the Spence Shale for the first time.
 The flap is larger and more complete than any reported from the Burgess
 Shale and allows for a better understanding of the morphology of Hurdia
 swimming flaps. A 3D model of a Hurdia frontal appendage indicates that
 there is only one morph of Hurdia frontal appendage found in both species,
 and apparent morphological differences between disarticulated appendages
 reflect a preservational continuum caused by varying oblique angles
 relative to the seafloor. Peytoia should no longer be reported from the
 Spence Shale, but its presence is confirmed in the Wheeler and Marjum
 formations. New mouthparts (oral cones) of Hurdia from the Spence Shale
 and Peytoia from the Marjum Formation with surface textures of
 submillimeter-diameter raised nodes are described. These new features have
 not been observed in material from the Burgess Shale and suggest slight
 differences in preservation.
description: NexusFileNexus file for phylogenetic analysis.PatesDaleyLieberman.nex
DOI: 10.15468/dl.qcs4sc
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Amomum longiligulare"
 ]
}

 The dataset includes 37 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001337-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.22mh6
title: Data from: Developmental plasticity of the stress response in female but not male guppies

description: To survive, animals must respond appropriately to stress. Stress responses
 are costly, so early-life experiences with potential stressors could
 adaptively tailor adult stress responses to local conditions. However, how
 multiple stressors influence the development of the stress response
 remains unclear, as is the role of sex. Trinidadian guppies (Poecilia
 reticulata) are small fish with extensive life history differences between
 the sexes and population variation in predation pressure and social
 density. We investigated how sex and early-life experience influence
 hormonal stress responses by manipulating conspecific density and
 perceived predation risk during development. In adults, we sampled
 cortisol twice to measure initial release and change over time in response
 to a recurring stressor. The sexes differed considerably in their
 physiological stress response. Males released more cortisol for their body
 mass than females and did not reduce cortisol release over time. By
 contrast, all females, except those reared at high density with predation
 cues, reduced cortisol release over time. Cortisol responses of males were
 less dynamic in response to current circumstances and early-life
 experiences than females, consistent with life history differences between
 the sexes. Our study underscores the importance of early-life experiences,
 interacting ecological factors, and sex differences in the organization of
 the stress response.
description: Chouinard-Thuly_cortisolData_ESMThis data file contained the raw data of a cortisol experiment. The data was collected in summary 2015. The guppies used in this experiment were reared in the laboratory under different developmental treatments, in a 2x2 design manipulating rearing density and predation levels. The README file explains the abbreviation of the columns.
DOI: 10.5061/dryad.9855v
title: Data from: Consequences of life history switch point plasticity for juvenile morphology and locomotion in the Túngara frog

description: Many animals with complex life cycles can cope with environmental
 uncertainty by altering the timing of life history switch points through
 plasticity. Pond hydroperiod has important consequences for the fitness of
 aquatic organisms and many taxa alter the timing of life history switch
 points in response to habitat desiccation. For example, larval amphibians
 can metamorphose early to escape drying ponds. Such plasticity may induce
 variation in size and morphology of juveniles which can result in
 carry-over effects on jumping performance. To investigate the carry-over
 effects of metamorphic plasticity to pond drying, we studied the Túngara
 frog, Physalaemus pustulosus, a tropical anuran that breeds in highly
 ephemeral habitats. We conducted an outdoor field mesocosm experiment in
 which we manipulated water depth and desiccation and measured time and
 size at metamorphosis, tibiofibula length and jumping performance. We also
 conducted a complimentary laboratory experiment in which we manipulated
 resources, water depth and desiccation. In the field experiment,
 metamorphs from dry-down treatments emerged earlier, but at a similar size
 to metamorphs from constant depth treatments. In the laboratory
 experiment, metamorphs from the low depth and dry-down treatments emerged
 earlier and smaller. In both experiments, frogs from dry-down treatments
 had relatively shorter legs, which negatively impacted their absolute
 jumping performance. In contrast, reductions in resources delayed and
 reduced size at metamorphosis, but had no negative effect on jumping
 performance. To place these results in a broader context, we review past
 studies on carry-over effects of the larval environment on jumping
 performance. Reductions in mass and limb length generally resulted in
 lower jumping performance across juvenile anurans tested to date.
 Understanding the consequences of plasticity on size, morphology and
 performance can elucidate the linkages between life stages.
description: meta_dataMeta-analysis datalab_dataData for the laboratory experimentField_experimentData from the field experiment
DOI: 10.5061/dryad.958f6
title: Data from: Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks

description: The evidence for adaptive phenotypic differentiation in mobile marine
 species remains scarce, partly due to the difficulty of obtaining
 quantitative genetic data to demonstrate the genetic basis of the observed
 phenotypic differentiation. Using a combination of phenotypic and
 molecular genetic approaches, we elucidated the relative roles of natural
 selection and genetic drift in explaining lateral plate number
 differentiation in threespine sticklebacks (Gasterosteus aculeatus) across
 the entire Baltic Sea basin (ca. 392 000 km2). We found that phenotypic
 differentiation (PST = 0.213) in plate number exceeded that in neutral
 markers (FST = 0.008), suggesting an adaptive basis for the observed
 differentiation. Since a close correspondence was found between plate
 phenotype and genotype at a QTL (STN381) tightly linked to the gene
 (Ectodysplasin) underlying plate variation, the evidence for adaptive
 differentiation was confirmed by comparison of FST at the QTL (FSTQ =
 0.089) with FST at neutral marker loci. Hence, the results provide a
 comprehensive demonstration of adaptive phenotypic differentiation in a
 high gene flow marine environment with direct, rather than inferred,
 verification for the genetic basis of this differentiation. In general,
 the results illustrate the utility of PST – FST – FSTQ comparisons in
 uncovering footprints of natural selection and evolution, and add to the
 growing evidence for adaptive genetic differentiation in high-gene flow
 marine environments, including that of the relatively young Baltic Sea.
description: Archive_JEBPlate counts and genotypes for STN381. Population codes are as follows in the publication.
DOI: 10.5061/dryad.h14r5
title: Data from: Environmental and genetic control of cold tolerance in the Glanville fritillary butterfly

description: Thermal tolerance has a major effect on individual fitness and species
 distributions, and can be determined by genetic variation as well as
 phenotypic plasticity. We investigate the effects of developmental and
 adult thermal conditions on cold tolerance, measured as chill coma
 recovery (CCR) time, during the early and late adult stage in the
 Glanville fritillary butterfly. We also investigate the genetic basis of
 cold tolerance by associating CCR variation with polymorphisms in
 candidate genes that have a known role in insect physiology. Our results
 demonstrate that a cooler developmental temperature leads to reduced cold
 tolerance in the early adult stage, whereas cooler conditions during the
 adult stage lead to increased cold tolerance. This suggests that adult
 acclimation, but not developmental plasticity, of adult cold tolerance is
 adaptive. This could be explained by the ecological conditions the
 Glanville fritillary experiences in the field, where temperature during
 early summer, but not spring, is predictive of thermal conditions during
 the butterfly’s flight season. In addition, an amino acid polymorphism
 (Ala-Glu) in the gene flightin, which has a known function in insect
 flight and locomotion, was associated with chill coma recovery. These
 amino acids have distinct biochemical properties and may thus affect
 protein function and/or structure. To our knowledge, our study is the
 first to link genetic variation in flightin to cold tolerance, or thermal
 adaptation in general.
description: deJong&Saastamoinen_Cold Tolerance_data_2018In this file are the development time, body mass, chill coma recovery and candidate gene SNP genotype data for all individuals used in the data analyses. Separate file is provided to explain in detail the column variablesdeJong&Saastaminen_Cold Tolerance_Column explanations_data_2018This file describes the column names used in data file 'deJong & Saastamoinen_ColdTolerance_data_2018-file'
DOI: 10.5061/dryad.5646p
title: Data from: Independent reversals to terrestriality in squirrels (Rodentia: Sciuridae) support ecologically mediated modes of adaptation

description: The family Sciuridae is one of the most widespread and ecologically
 diverse lineage of rodents and represents an ideal model for investigating
 the evolution of locomotion modes and the historical biogeography of
 terrestrial mammals. We used a comprehensive database on locomotion modes,
 an updated phylogeny and novel biogeographic comparative methods to
 re-assess the evolution of locomotion of squirrels and to investigate if
 these locomotion modes evolved convergently in different continents. We
 found that locomotion changes occurred in different independent lineages
 of the family, including four reversals to terrestriality and one
 evolution of gliding. We also found evidence for Eurasia as the center of
 origin of Sciuridae, challenging the classification of the oldest squirrel
 fossil records from the early Oligocene in North America. Additionally,
 Eurasia is also the possible center of origin for most of squirrel
 sub-families and tribes, and where locomotion changes have occurred.
 Parallel locomotion shifts could be explained by the adaptation towards
 different ecological niches followed by colonization of new continents.
description: Locomotion modes and
 geographic distribution ranges of 184 species of
 Sciuroidea.We collected locomotion
 data of 184 species of Sciuridae and one species of its sister family
 Aplodontidae. We used Nowak (1999) as the main source of information of
 squirrel locomotion modes, and when needed we complemented this
 information with more specific bibliography (Emmons, 1980; Musser et al.,
 2010; Lim & Yeo, 2012). We followed Steppan et al. (2004) and assigned
 each species to one of the following categories: gliding (species with the
 ability to glide with the help of extending membranes), arboreal (species
 that live and nest in trees, even if spending some time on the ground),
 intermediate (species that spend most of the time on the ground, but can
 also spend some time in trees being good climbers), and terrestrial
 (species that live and nest on the ground, seldom if ever climbing). We
 also assigned species to one or more continental landmasses: Africa,
 Eurasia, North and Central America, and South America. This was based on
 the current distribution of species compiled by the IUCN (Schipper et al.
 2008; data downloaded on December 2015).SupplementaryInformationS1_TableS1.docx.xlsx
DOI: 10.5061/dryad.4782m
title: Data from: Environmental complexity and the purging of deleterious alleles

description: Sexual interactions among adults can generate selection on both males and
 females with genome-wide consequences. Sexual selection through males is
 one component of this selection that has been argued to play an important
 role in purging deleterious alleles. A common technique to assess the
 influence of sexual selection is by a comparison of experimental evolution
 under enforced monogamy vs. polygamy. Mixed results from past studies may
 be due to the use of highly simplified lab conditions that alter the
 nature of sexual interactions. Here we examine the rate of purging of 22
 gene disruption mutations in experimental polygamous populations of
 Drosophila melanogaster in each of two mating environments: a simple, high
 density environment (i.e., typical fly vials) and a lower density, more
 spatially complex environment. Based on past work, we expect sexual
 interactions in the latter environment to result in stronger selection in
 both sexes. Consistent with this, we find that mutations tend to be purged
 more quickly in populations evolving in complex environments. We discuss
 possible mechanisms by which environmental complexity might modulate the
 rate at which deleterious alleles are purged and putatively ascribe a role
 for sexual interactions in explaining the treatment differences in our
 experiment.
description: Test crosses to
 determine mutant allele frequency in experimental
 populationsThis file contains data
 from test crosses conducted to determine wildtype and mutant (gene
 disruption mutations) allele frequencies in replicate populations
 experimentally evolving in either a complex or simple mating environment.
 The data counts of are the inferred genotypes of males sampled at various
 time points (generations) over the course of the experiment. Each row
 corresponds to data from a single set of test crosses for a particular
 replicate population. Columns correspond to the following: generation:
 generation in which test cross was performed (note: no test crosses were
 performed at generation 0; rather replicates were established with
 individuals of known genotype); stock.number: corresponds to the stock
 number from the Bloomington Drosophila Stock Center (as of September
 2014); experimental.code: corresponds to the experimental ID given to the
 mutant allele (also corresponds to the ID column in the supplemental
 materials); treatment: corresponds to the mating treatment (simple vs.
 complex); replicate: replicate population within treatment; heterozygote:
 number of heterozygote males sampled; wildtype: number of homozygous
 wildtype males sampled; mutant: number of homozygous mutant
 (gene-disruption mutation) males sampled.evolution_experiment_data.csv
DOI: 10.5061/dryad.cv87j
title: Data from: Eocene Pachynolophinae (Perissodactyla, Palaeotheriidae) from China and their paleobiogeographic implications

description: The Eocene Palaeotheriidae was traditionally considered a nearly endemic
 European group within Equoidea, but a few palaeotheres have been reported
 from Asia. Here I reanalyze a maxilla containing M1-3 from the Lunan
 Basin, Yunnan Province, China. This element was initially assigned to a
 new tapiromorph species, Lophialetes yunnanensis, but I erect a new genus
 Lophiohippus within Pachynolophinae for the Yunnan specimen based mainly
 on the absence of mesostyles, the strongly inclined metalophs, the strong
 development of lophodonty, parastyles overlapping metastyles of preceding
 teeth and situated mesial to the paracone, and the fact that M3 is longer
 than wide and has a large and buccally deflected metastyle. L. yunnanensis
 differs from European Anchilophus and Paranchilophus in that the
 parastyles are situated mesial or even slightly lingual, rather than
 mesiobuccal, to the paracones, and M3 is relatively pronouncedly larger
 than M1. I further reanalyze Qianohippus magicus from the Shinao Basin of
 Guizhou Province, China, in which the complete dentition is known.
 Qianohippus is characterized by a molariform P2 and non-molariform P3-4; a
 relatively high degree of lophodonty; the absence of mesostyles; an
 angular bending in the protoloph on P3-M3 and the metaloph on M1-3 at the
 paraconule and metaconule, respectively; and weakly developed “metastylid”
 on the lower cheek teeth. A cladistic analysis supports a close
 relationship between Lophiohippus yunnanensis and Paranchilophus, and
 suggests that Qianohippus is closely related to some derived pachynolophs.
 The appearance of the pachynolophins Lophiohippus and Qianohippus in China
 supports the existence of a biogeographic connection between Europe and
 Asia in the Middle-Late Eocene, and the dispersal route was probably along
 the Tethyan micro-continents in the south.
description: Bai_European
 equoids_FThe matrix was based on
 data from Danilo et al. (2013:
 https://doi.org/10.1080/02724634.2012.711404), with Lophiohippus
 yunnanensis and Qianohippus magicus added, and contained a total of 28
 taxa and 72 characters
DOI: 10.5061/dryad.dr4683b
title: Data from: Plasticity in leaf litter traits partly mitigates the impact of thinning on forest floor carbon cycling

description: 1. Reducing stand density by thinning intensification has been emphasized
 as an efficient strategy of forest adaptation to climate change as it
 improves stand resistance to drought. Yet, it is still unclear how it
 could affect litter C cycling processes. Recent evidence indicates that
 the plasticity of an oak tree species can lead to a decline in its leaf
 litter quality and decomposability following thinning. The consequences
 for litter decomposition and forest floor C storage at the ecosystem-scale
 remain largely unexplored. 2. In this study, we took advantage of a
 regional-scale, multi-site network of long-term thinning experiments in
 temperate oak (Quercus petraea) forests to address this issue. We measured
 ecosystem properties related to forest floor C cycling in 19 plots across
 eight experimental sites covering a large gradient of stand density and
 age. Though we expected thinning to affect in situ litter decomposition by
 altering oak leaf litter quality, we conducted complementary experiments
 exploring additional mechanisms, i.e. alterations of microenvironmental
 conditions and soil faunal activity. 3. Thinning intensification induced a
 strong decline in tree canopy leaf area index, aboveground tree litter
 production and forest floor decomposition rate in early ‘aggradation’
 stage of forest development. This slower litter decomposition was mainly
 driven by plasticity of oak trees that produced leaf litter of poorer
 quality and decomposability following thinning, e.g. litter richer in
 secondary metabolites such as condensed tannins. Change in
 microenvironmental conditions also contributed to the slowdown of litter
 decomposition, likely as a result of the less buffered microclimate
 associated with larger tree canopy opening. No change in soil faunal
 effect induced by thinning was found. 4. Thinning resulted in a limited
 decrease in forest floor C stock. Indeed, the slower litter decomposition
 offset nearly half of the forest floor C loss associated to the reduced
 litterfall in ‘aggradation’ stage. 5. Our study demonstrated that
 phenotypic plasticity in leaf litter traits of a dominant tree species can
 strongly affect ecosystem functioning by slowing forest floor
 decomposition following thinning intensification, in turn partly
 mitigating the negative effect of thinning on forest floor C storage.
description: Thinning effect on
 forest floor C cyclingThis file includes data
 about the experimental plots characteristics, forest canopy structure,
 canopy tree litter production, litter decomposition processes and forest
 floor properties.Henneron_et_al._Functional
 Ecology_2018_Dataset.xlsx
DOI: 10.5061/dryad.t2hh6tj
title: Data from: The effects of lateral line ablation and regeneration in schooling giant danios

description: Fish use multiple sensory systems, including vision and their lateral line
 system, to maintain position and speed within a school. Although previous
 studies have shown that ablating the lateral line alters schooling
 behavior, no one has examined how the behavior recovers as the sensory
 system regenerates. We studied how schooling behavior changes in giant
 danios Devario aequipinnatus when their lateral line system is chemically
 ablated and after the sensory hair cells regenerate. We found that fish
 could school normally immediately after chemical ablation, but that they
 had trouble schooling one to two weeks after the chemical treatment, when
 the hair cells had fully regenerated. We filmed groups of giant danios
 with two high-speed cameras and reconstructed the 3D positions of each
 fish within a group. One fish in the school was treated with gentamycin to
 ablate all hair cells. Both types of neuromasts, canal and superficial,
 were completely ablated after treatment but fully regenerated after one
 week. We quantified the structure of the school using nearest neighbor
 distance, bearing, elevation, and the cross-correlation of velocity
 between each pair of fish. Treated fish maintained a normal position
 within the school immediately after the lateral line ablation, but could
 not school normally one or two weeks after treatment, even though the
 neuromasts had fully regenerated. By four to eight weeks post-treatment,
 the treated fish could again school normally. These results demonstrate
 that the behavioral recovery after lateral line ablation is a longer
 process than the regeneration of the hair cells themselves.
description: Position measurements
 from schooling giant daniosThe data file contains
 the processed data for each individual fish measured at each time point.
 The data is categorized by treatment and week number. Treatment describes
 the type of chemical used to ablate the lateral line system. Week
 describes the treatment groups and the time point through eight weeks. The
 five main metrics described in our paper are the following: nearest
 neighbor distance or NND (unit: body length), time in school (percentage),
 angular bearing (unit: degrees), angular elevation (unit: degrees), and
 speed (body length per second).JEXBIO-2017-175166-Processed-Data-Master.txt