cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.04gj1
title: Data from: Compositional turnover and ecological changes related to the waxing and waning of glaciers during the Late Paleozoic ice age in ice-proximal regions (Pennsylvanian, western Argentina)

description: The late Paleozoic ice age (LPIA) had a profound effect on the biota.
 Despite much research having been focused on paleotropical regions or
 global-scale analyses, regional ecological changes have seldom been
 studied in ice-proximal basins. Here, I study the compositional turnover
 and diversity structure across the main Carboniferous glacial event
 recorded in western Argentina and the subsequent nonglacial interval.
 Brachiopod and bivalve data from western Argentina suggest that the
 transition from glacial to nonglacial climates caused major compositional
 changes. Turnover, however, was not uniform across the bathymetric
 gradient, being higher in deep environments. Because extirpation was
 concentrated in brachiopods, but immigration was similar in both clades,
 the taxonomic structure of the region was significantly modified. Although
 regional hierarchical diversity structure and occupancy distributions
 remained stable, dissecting the analysis in brachiopods and bivalves
 underscores that both clades had different responses to climate change.
 Brachiopods, on the one hand, show stability in the diversity structure
 and a very slight decrease in occupancies of intermediate genera, while
 bivalves show an important rise in diversity, both at the environment and
 regional scale, and an increase in genera with intermediate occupancies.
 The bathymetric diversity gradient was also modified from hump shaped with
 maximum diversity in the deep subtidal to a linear gradient with maximum
 values toward the offshore. However, relative compositional differences
 within environments remained stable, with maximum values at intermediate
 depths both in glacial and nonglacial intervals. Moreover, local-scale
 coexistence between brachiopods and bivalves changed in the nonglacial
 interval, showing significant segregation, which indicates relevant
 modifications in community assembly dynamics. Results from western
 Argentina highlight the magnitude of regional-scale ecological changes
 during the LPIA in ice-proximal regions, suggesting that the waxing and
 waning of glaciers was able to cause regional taxonomic turnover and
 medium-scale ecological changes even during intervals of relative
 macroevolutionary quiescence.
description: DatasetPresence-Absence dataset of bed-level resolution samples from the Bashkirian and Moscovian-Kasimovian of Western Argentinadataset.xlsSystematic classificationSystematic classification of each genus used in the analysessist_data.xlsList of TaxaList of genera present in each studied interval (i.e. Bashkirian or Moscovian-Kasimovian)supplementary list of taxa.doc
DOI: 10.5061/dryad.6n5s3
title: Data from: Fine tuning for the tropics: application of eDNA technology for invasive fish detection in tropical freshwater ecosystems.

description: Invasive species pose a major threat to aquatic ecosystems. Their impact
 can be particularly severe in tropical regions, like those in northern
 Australia, where &gt;20 invasive fish species are recorded. In
 temperate regions, environmental DNA (eDNA) technology is gaining momentum
 as a tool to detect aquatic pests, but the technology’s effectiveness has
 not been fully explored in tropical systems with their unique climatic
 challenges (i.e. high turbidity, temperatures and ultra-violet light). In
 this study, we modified conventional eDNA protocols for use in tropical
 environments using the invasive fish, Mozambique tilapia (Oreochromis
 mossambicus) as a detection model. We evaluated the effects of high water
 temperatures and fish density on the detection of tilapia eDNA, using
 filters with larger pores to facilitate filtration. Large–pore filters (20
 μm) were effective in filtering turbid waters and retaining sufficient
 eDNA, whilst achieving filtration times of 2-3 minutes per 2-L sample.
 High water temperatures, often experienced in the tropics (23, 29, 35 °C),
 did not affect eDNA degradation rates, although high temperatures (35 °C)
 did significantly increase fish eDNA shedding rates. We established a
 minimum detection limit for tilapia (1 fish/ 0.4 megalitres/ after 4 days)
 and found that low water flow (3.17 L/s) into ponds with high fish density
 (&gt;16 fish/ 0.4 megalitres) did not affect eDNA detection. These
 results demonstrate that eDNA technology can be effectively used in
 tropical ecosystems to detect invasive fish species.
description: Exp1_DATA_FilterSize_PreFilterPresence/absence data for filtration experiment 1 using 3, 10 and 20 um filters, with and without a prefiltering step.Exp2_DATA_eDNAsheddingInitial tilapia eDNA concentrations in ng at the start of Exp 2 on degradation for all three treatments, 23, 29 and 35 degrees Celcius.Exp2_DATA_TMP_DegredationPresence/absence data for Exp 2 on degradation of tilapia eDNA for 3 treatments of temperature 23,29 and 35 degrees Celcius.Exp3_DATA_Density_Time_FlowPresence/absence data recorded as probability of detection for all qPCR replicates by day for all treatment pond densities (0,1,2,4,8,16,32, and up to 64 fish) for Experiment 3-Accumulation of tilapia eDNA.
DOI: 10.5061/dryad.p9q57
title: Data from: Generalized selection to overcome innate immunity selects for host breadth in an RNA virus

description: Virus-host co-evolution has selected for generalized host defense against
 viruses, exemplified by interferon production/signaling and other innate
 immune function in eukaryotes such as humans. Although cell-surface
 binding primarily limits virus infection success, generalized adaptation
 to counteract innate immunity across disparate hosts may contribute to RNA
 virus emergence potential. We examined this idea using vesicular
 stomatitis virus (VSV) populations prevoously evolved on strictly immune
 deficient (HeLa) cells, strictly immune competent (MDCK) cells, or on
 alternating deficient/competent cells. By measuring viral fitness in
 unselected human cancer cells of differing innate immunity, we confirmed
 that HeLa-adapted populations were specialized for innate immune-deficient
 hosts, whereas MDCK-adapted populations were relatively more generalized
 for fitness on hosts of differing innate immune capacity and of different
 species origin. We also confirmed that HeLa-evolved populations maintained
 fitness in immune-deficient non-human primate cells. These results suggest
 that innate immunity is more prominent than host species in determining
 viral fitness at the host-cell level. Finally, our prediction was inexact
 that selection on alternating deficient/competent hosts should produce
 innate viral generalists. Rather, fitness differences among alternating
 host-evolved VSV populations indicated variable capacities to evade innate
 immunity. Our results suggest that the evolutionary history of innate
 immune selection can affect whether RNA viruses evolve greater
 host-breadth.
description: Figure 2. B)
 Measurements of IFN-β gene induction in HeLa and MDCK cells via
 qPCRThis is the data
 corresponding to figure 2B, which describes the relative transcript levels
 of IFBN-beta in MDCK and HeLa cells after infection with VSV
 M51R.Fig2B_IFNbqPCR.xlsxFig 3. A-C) Quantification of IFN response in PC-3 and LNCaP cellsThis file includes the data for Figure 3 A-C. Fig. 3A includes the data for IFN-b secretion by PC3 and LnCap cells after VSV infection, as measured by ELISA. Figure 3B-C) has the normalized transcript quantities for MXA and OAS1 after stimulation with IFN-b, as measured by RT-qPCR.Fig3A-C_IFNbresponse.xlsxFigure 5. Selection in temporally heterogeneous innate immune environments leads to VSV strains with differential capacities to block IFN-β production.This data corresponds to the graph in Figure 5. It describes the secretion of IFN-b in PC3 cells (as measured by ELISA) after infection with different strains of VSV experimentally evolved in heterogeneous innate immune environments.Fig5_AltPop.xlsx
DOI: 10.5061/dryad.5j354
title: Data from: Crop domestication facilitated rapid geographical expansion of a specialist pollinator, the squash bee Peponapis pruinosa

description: Squash was first domesticated in Mexico and is now found throughout North
 America (NA) along with Peponapis pruinosa, a pollen specialist bee
 species of the squash genus Cucurbita. The origin and spread of squash
 cultivation is well-studied archaeologically and phylogenetically;
 however, no study has documented how cultivation of this or any other crop
 has influenced species in mutualistic interactions. We used molecular
 markers to reconstruct the demographic range expansion and colonization
 routes of P. pruinosa from its native range into temperate NA. Populations
 east of the Rocky Mountains expanded from the wild host plant's range
 in Mexico and were established by a series of founder events. Eastern
 North America was most likely colonized from squash bee populations in the
 present-day continental Midwest USA and not from routes that followed the
 Gulf and Atlantic coasts from Mexico. Populations of P. pruinosa west of
 the Rockies spread north from the warm deserts much more recently, showing
 two genetically differentiated populations with no admixture: one in
 California and the other one in eastern Great Basin. These bees have
 repeatedly endured severe bottlenecks as they colonized NA, following
 human spread of their Cucurbita pollen hosts during the Holocene.
description: Lopez-Uribe-etal_Genepop-Peponapis-GenotypesGenotype data for the 942 individuals included in the analysis. File is in genepop format.Lopez-Uribe_Peponapis-Geographic-InformationThis excel file contains detailed geographic information for all individuals used in the genetic analysis.
DOI: 10.5061/dryad.gm21j
title: Data from: Habitat specialization and climate affect arthropod fitness: a comparison of generalist vs. specialist spider species in Arctic and temperate biomes

description: Life history trade-offs are a key notion in evolutionary biology, notably
 for understanding how selection shapes the diversity of traits among
 species. Despite the frequent study of such trade-offs, few studies
 synchronously investigate the effects of multiple factors, such as niche
 specialization and adaptation to harsh environments. We compared
 reproduction (fecundity and egg quality) in two sympatric couples (one
 habitat generalist and one specialist) of congeneric wolf spider species,
 in both Arctic and temperate habitats. We found that specialist species at
 both latitudes invested more in clutch size than did generalist species.
 We interpret this result as an optimization of clutch production. In the
 Arctic, the specialist was able to invest in fecundity with increasing
 body size at a much higher rate than the generalist species. In the
 temperate habitat, both species showed similar strategies: they increased
 quantity and quality of offspring relative to body size at the same rate.
 These results are consistent with the hypothesis that Arctic species must
 develop distinct strategies in order not to overlap each other’s
 ecological niches as a consequence of limited food resources or niche
 space. We emphasize the need to test the role of plasticity and
 environmentally mediated effects of competition on arthropod fitness.
description: data_Ameline_etal_2017_BJLS
DOI: 10.5061/dryad.nh1r171j
title: Data from: Are dormant plants hedging their bets? Demographic consequences of prolonged dormancy in variable environments

description: During the growing season, some individuals in perennial plant populations
 may remain alive below ground while others emerge. This phenomenon, known
 as prolonged dormancy, seems maladaptive, because prolonged dormancy
 delays growth and reproduction. However, prolonged dormancy may offer the
 benefit of safety while below ground, leading to the hypothesis that
 prolonged dormancy is a bet hedging strategy. We evaluated this hypothesis
 using a 25-year demographic study of Astragalus scaphoides, an iteroparous
 perennial plant. First, we determined the relationship between prolonged
 dormancy and fitness using data from individuals in our population. This
 analysis showed that prolonged dormancy decreased arithmetic mean fitness
 and reduced variance in fitness. Geometric mean fitness was maximized at
 intermediate levels of prolonged dormancy. Empirical patterns of lifetime
 reproductive success confirm this relationship. We also compared fitness
 of plants in our population to hypothetical plants without prolonged
 dormancy, which generally revealed benefits of prolonged dormancy, even if
 plants could forego prolonged dormancy without costs to other vital rates.
 Therefore, prolonged dormancy may indeed function as a bet hedging
 strategy, but the benefits of remaining below ground only outweigh the
 costs for a subset of individuals. Bet hedging has been demonstrated in
 plants with simple life histories, such as annuals and monocarpic
 perennials; we present evidence that bet hedging may be important for
 plants with more complex life histories.
description: Astragalus scaphoides
 fatesAstragalus scaphoides
 fruits.
DOI: 10.5061/dryad.rt730
title: Data from: Phenological synchrony between a butterfly and its host plants: experimental test of effects of spring temperature

description: 1. Climate-driven changes in the relative phenologies of interacting
 species may potentially alter the outcome of species interactions. 2.
 Phenotypic plasticity is expected to be important for short-term response
 to new climate conditions, and differences between species in plasticity
 are likely to influence their temporal overlap and interaction patterns.
 As reaction norms of interacting species may be locally adapted, any such
 climate-induced change in interaction patterns may vary among localities.
 However, consequences of spatial variation in plastic responses for
 species interactions are understudied. 3. We experimentally explored how
 temperature affected synchrony between spring emergence of a butterfly,
 Anthocharis cardamines, and onset of flowering of five of its host plant
 species across a latitudinal gradient. We also studied potential effects
 on synchrony if climate-driven northward expansions would be faster in the
 butterflies than in host plants. Lastly, to assess how changes in
 synchrony influence host use we carried out an experiment to examine the
 importance of the developmental stage of plant reproductive structures for
 butterfly oviposition preference. 4. In southern locations the butterflies
 were well-synchronized with the majority of their local host plant species
 across temperatures, suggesting that thermal plasticity in butterfly
 development matches oviposition to host plant development and that thermal
 reaction norms of insects and plants result in similar advancement of
 spring phenology in response to warming. In the most northern region,
 however, relative phenology between the butterfly and two of its host
 plant species changed with increased temperature. We also show that the
 developmental stage of plants was important for egg-laying, and conclude
 that temperature-induced changes in synchrony in the northernmost region
 are likely to lead to shifts in host use in A. cardamines if spring
 temperatures become warmer. Northern expansion of butterfly populations
 might possibly have a positive effect on keeping up with host plant
 phenology with more northern host plant populations. 5. Considering that
 the majority of insect herbivores exploit multiple plant species differing
 in their phenological response to spring temperatures, temperature-induced
 changes in synchrony might lead to shifts in host use and changes in
 species interactions in many temperate communities.
description: experimental data used
 for analyses in the paperAll data
 file.xlsx
DOI: 10.5061/dryad.t87f0
title: Data from: Community- weighted mean plant traits predict small scale distribution of insect root herbivore abundance

description: Small scale distribution of insect root herbivores may promote plant
 species diversity by creating patches of different herbivore pressure.
 However, determinants of small scale distribution of insect root
 herbivores, and impact of land use intensity on their small scale
 distribution are largely unknown. We sampled insect root herbivores and
 measured vegetation parameters and soil water content along transects in
 grasslands of different management intensity in three regions in Germany.
 We calculated community-weighted mean plant traits to test whether the
 functional plant community composition determines the small scale
 distribution of insect root herbivores. To analyze spatial patterns in
 plant species and trait composition and insect root herbivore abundance we
 computed Mantel correlograms. Insect root herbivores mainly comprised
 click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated
 grasslands. Total insect root herbivore numbers were positively related to
 community-weighted mean traits indicating high plant growth rates and
 biomass (specific leaf area, reproductive- and vegetative plant height),
 and negatively related to plant traits indicating poor tissue quality
 (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently,
 were also positively related to high plant growth rates and furthermore to
 root dry mass, but were not related to tissue quality. Insect root
 herbivore numbers were not related to plant cover, plant species richness
 and soil water content. Plant species composition and to a lesser extent
 plant trait composition displayed spatial autocorrelation, which was not
 influenced by land use intensity. Insect root herbivore abundance was not
 spatially autocorrelated. We conclude that in semi-natural grasslands with
 a high share of generalist insect root herbivores, insect root herbivores
 affiliate with large, fast growing plants, presumably because of
 availability of high quantities of food. Affiliation of insect root
 herbivores with large, fast growing plants may counteract dominance of
 those species, thus promoting plant diversity.
description: PLOSONEdataPLOSONEDATA.zip
DOI: 10.5061/dryad.kp74v
title: Data from: Artificial selection on male genitalia length alters female brain size

description: Male harassment is a classic example of how sexual conflict over mating
 leads to sex-specific behavioural adaptations. Females often suffer
 significant costs from males attempting forced copulations, and the sexes
 can be in an arms race over male coercion. Yet, despite recent recognition
 that divergent sex-specific interests in reproduction can affect brain
 evolution, sexual conflict has not been addressed in this context. Here,
 we investigate whether artificial selection on a correlate of male success
 at coercion, genital length, affects brain anatomy in males and females.
 We analysed the brains of eastern mosquitofish (Gambusia holbrooki), which
 had been artificially selected for long or short gonopodium, thereby
 mimicking selection arising from differing levels of male harassment. By
 analogy to how prey species often have relatively larger brains than their
 predators, we found that female, but not male, brain size was greater
 following selection for a longer gonopodium. Brain subregion volumes
 remained unchanged. These results suggest that there is a positive genetic
 correlation between male gonopodium length and female brain size, which is
 possibly linked to increased female cognitive ability to avoid male
 coercion. We propose that sexual conflict is an important factor in the
 evolution of brain anatomy and cognitive ability.
description: Data_Buechel et al.
 2016. Artificial selection on male genitalia length alters female brain
 sizeFull data on total brain
 weight (mg) and the volumes (mm3) of brain substructures of
 gonopodium-selected mosquitofish (G.holbrooki).Dryad
 upload.xlsx
DOI: 10.15468/dl.8szym8
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Festuca nuda"
 ]
}

 The dataset includes 58 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000800-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7120d
title: Data from: Reduced sexual dichromatism, mutual ornamentation, and individual quality in the monogamous Zenaida dove, Zenaida aurita

description: Although variation in plumage coloration is known to occur both between
 and within sexes, its study remains limited to a few bird families. The
 Zenaida dove, Zenaida aurita, is a socially monogamous tropical columbid
 bird species, characterized by an overall cinnamon-brownish plumage and
 structural colorations on the head and neck. The species has been
 described as sexually dichromatic for plumage, although color differences
 between males and females are not obvious in the field. We investigated
 variation in the presumably melanin-based color of the crown, mantle,
 breast, and belly, in the iridescent dark-blue streaks on the head, and in
 the symmetric iridescent patches on the neck, over the whole spectrum
 visible to birds. Further, unlike most previous studies, we assessed
 covariation between plumage color and phenotypic traits in both males and
 females in relation to the putative signaling function of ornaments.
 Zenaida doves appeared to be slightly sexually dichromatic for the hue of
 pigment-based colored areas, with males being on average more reddish than
 females. However, this difference was not discernible when considering the
 avian visual system. Conversely, although the reflectance spectra of
 iridescent plumage did not significantly differ between sexes in
 brightness, chroma or spectral position of the peaks, color discrimination
 analyses showed that individuals should be able to perceive between- or
 within-sex differences in the color of the iridescent patch. In addition,
 several color parameters of brown and iridescent feathers were
 significantly related to territorial status, body condition, wing chord,
 and, albeit weakly, to individual multilocus heterozygosity. Overall, our
 results thus suggest that plumage color might be a reliable signal of
 quality in individuals of both sexes in this species. Further studies are
 needed to test the potential implication of plumage coloration in mate
 choice and mating patterns in the Zenaida Dove.
description: JAV-00902.R3_rawdataIndividual ID, Year, Season, Session, Plumage colour variables, Sex, Territorial status, Heterozygosity, Wing chord length, Body mass, Body condition