cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r7bn134
title: Data from: Predictors of Phytophthora diversity and community composition in natural areas across diverse Australian ecoregions

description: Comprehensive understanding of the patterns and drivers of microbial
 diversity at a landscape scale is in its infancy, despite the recent ease
 by which soil communities can be characterized using massively parallel
 amplicon sequencing. Here we report on a comprehensive analysis of the
 drivers of diversity distribution and composition of the ecologically and
 economically important Phytophthora genus from 414 soil samples collected
 across Australia. We assessed 22 environmental and seven categorical
 variables as potential predictors of Phytophthora species richness, αandβ
 diversity, including both phylogenetically and non‐phylogenically explicit
 methods. In addition, we classified each species as putatively native or
 introduced and examined the distribution with respect to putative origin.
 The two most widespread species, P. multivora and P. cinamomi, are
 introduced, though five of the ten most widely distributed species are
 putatively native. Introduced taxa comprised over 54% of Australia's
 Phytophthora diversity and these species are known pathogens of annual and
 perennial crop habitats as well as urban landscapes and forestry. Patterns
 of composition were most strongly predicted by bioregion (R2=0.29) and
 ecoregion (R2=0.26) identity; mean precipitation of warmest quarter, mean
 temperature of the wettest quarter and latitude were also highly
 significant and described approximately 21%, 14% and 13% of variation in
 NMDS composition, respectively. We also found statistically significant
 evidence for phylogenetic over‐dispersion with respect to key climate
 variables.This study provides a strong baseline for understanding
 biogeographical patterns in this important genus as well the impact of key
 plant pathogens and invasive Phytophthora species in natural ecosystems.
description: Species and
 environmental matrixThis file contains three
 spreadsheets (1) the presence/absence data of Phytophthora species by site
 (2) the environmental matrix/categories and (3) the species
 informationBurgess et al
 2018_Ecography_Dryad.xlsx
DOI: 10.5061/dryad.j7h0c
title: Data from: Stabilising selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci

description: The loci arginine vasopressin receptor 1a (avpr1a) and oxytocin receptor
 (oxtr) have evolutionarily conserved roles in vertebrate social and sexual
 behavior. Allelic variation at a microsatellite locus in the 5’ regulatory
 region of these genes is associated with fitness in the bank vole Myodes
 glareolus. Given the low frequency of long and short alleles at these
 microsatellite loci in wild bank voles, we used breeding trials to
 determine whether selection acts against long and short alleles. Female
 bank voles with intermediate length avpr1a alleles had the highest
 probability of breeding, while male voles whose avpr1a alleles were very
 different in length had reduced probability of breeding. Moreover, there
 was a significant interaction between male and female oxtr genotypes,
 where potential breeding pairs with dissimilar length alleles had reduced
 probability of breeding. These data show how genetic variation at
 microsatellite loci associated with avpr1a and oxtr is associated with
 fitness, and highlight complex patterns of selection at these loci. More
 widely, these data show how stabilising selection might act on allele
 length frequency distributions at gene-associated microsatellite loci.
description: Breeding data associated
 with microsatellite allele lengthData are records of all
 attempted breedings of bank voles, and information about microsatellite
 allele length at two loci (Avpr1a and oxtr), and also information about
 litter size.MsatBreedingSuccess_PRSOCB.txt
DOI: 10.5061/dryad.cf426
title: Data from: Honey bee inhibitory signaling is tuned to threat severity and can act as a colony alarm signal

description: Alarm communication is a key adaptation that helps social groups resist
 predation and rally defenses. In Asia, the world's largest hornet,
 Vespa mandarinia, and the smaller hornet, Vespa velutina, prey upon
 foragers and nests of the Asian honey bee, Apis cerana. We attacked
 foragers and colony nest entrances with these predators and provide the
 first evidence, in social insects, of an alarm signal that encodes graded
 danger and attack context. We show that like A. mellifera, A. cerana
 possesses a vibrational "stop signal", which can be triggered by
 predator attacks upon foragers, and inhibits waggle dancing. Large hornet
 attacks were more dangerous and resulted in higher bee mortality. Per
 attack at the colony-level, large hornets elicited more stop signals than
 small hornets. Unexpectedly, stop signals elicited by large hornets (SS
 large hornet) had a significantly higher vibrational fundamental frequency
 than those elicited by small hornets (SS small hornet) and were more
 effective at inhibiting waggle dancing. Stop signals resulting from
 attacks upon the nest entrance (SS nest) were produced by foragers and
 guards and were significantly longer in pulse duration than stop signals
 elicited by attacks upon foragers (SS forager). Unlike SS forager, SS nest
 were targeted at dancing and non-dancing foragers and had the common
 effect, tuned to hornet threat level, of inhibiting bee departures from
 the safe interior of the nest. Meanwhile, nest defenders were triggered by
 bee alarm pheromone and live hornet presence to heatball the hornet. In A.
 cerana, the waggle dance, sophisticated recruitment communication that
 encodes food location, is therefore matched with an inhibitory/alarm
 signal that encodes information about the context of danger and its threat
 level.
description: AceranaSSDataFinalPLOSBioEach tab in this excel sheet corresponds to a figure in the paper.Dryad metadata file.docx
DOI: 10.5061/dryad.6455c
title: Data from: Reverse audience effects on helping in cooperatively breeding marmoset monkeys

description: Cooperatively breeding common marmosets show substantial variation in the
 amount of help they provide. Pay-to-stay and social prestige models of
 helping attribute this variation to audience effects, i.e. that
 individuals help more if group members can witness their interactions with
 immatures, whereas models of kin selection, group augmentation, or ones
 stressing the need to gain parenting experience do not predict any
 audience effects. We quantified the readiness of adult marmosets to share
 food in the presence or absence of other group members. Contrary to both
 predictions we found a reverse audience effect on food sharing behaviour:
 marmosets would systematically share more food with immatures when no
 audience was present. Thus, helping in common marmosets, at least in
 related family groups, does not support the pay-to-stay or the social
 prestige model, and helpers do not take advantage of the opportunity to
 engage in reputation management. Rather, the results appear to reflect a
 genuine concern for the immatures' wellbeing, which seems
 particularly strong when solely responsible for the immatures.
description: Food sharing
 datasetExcel table with raw
 data of common marmosets behavior during food sharing
 experiment.rawdata_foodsharing_datarepositry.xlsx
DOI: 10.5061/dryad.s20hm
title: Data from: The evolution of clutch size in hosts of avian brood parasites

description: Coevolution with avian brood parasites shapes a range of traits in their
 hosts, including morphology, behavior, and breeding systems. Here we
 explore whether brood parasitism is also associated with the evolution of
 host clutch size. Several studies have proposed that hosts of highly
 virulent parasites could decrease the costs of parasitism by evolving a
 smaller clutch size, because hosts with smaller clutches will lose fewer
 progeny when their clutch is parasitized. We describe a model of the
 evolution of clutch size, which challenges this logic and shows instead
 that an increase in clutch size (or no change) should evolve in hosts. We
 test this prediction using a broad-scale comparative analysis to ask
 whether there are differences in clutch size within hosts and between
 hosts and nonhosts. Consistent with our model, this analysis revealed that
 host species do not have smaller clutches and that hosts that incur larger
 costs from raising a parasite lay larger clutches. We suggest that brood
 parasitism might be an influential factor in clutch-size evolution and
 could potentially select for the evolution of larger clutches in host
 species.
description: All_database2017_clutchDatabase containing all traits used in comparative analyses.the first tab contains the metadata and the second one contains the datatable used as input in R.Dryad_Code_ClutchSizeR code used for comparative analyses.
DOI: 10.5061/dryad.sj894
title: Data from: Does mating behaviour affect connectivity in marine fishes? Comparative population genetics of two protogynous groupers (Family Serranidae)

description: Pelagic larval duration (PLD) has been hypothesized to be the primary
 predictor of connectivity in marine fishes; however, few studies have
 examined the effects that adult reproductive behaviour may have on
 realized dispersal. We assessed gene flow (connectivity) by documenting
 variation in microsatellites and mitochondrial DNA sequences in two
 protogynous species of groupers, the aggregate spawning red hind,
 Epinephelus guttatus, and the single-male, harem-spawning coney,
 Cephalopholis fulva, to ask if reproductive strategy affects connectivity.
 Samples of both species were obtained from waters off three islands
 (Puerto Rico, St. Thomas, and St. Croix) in the Caribbean Sea. Despite the
 notion that aggregate spawning of red hind may facilitate larval
 retention, stronger signals of population structure were detected in the
 harem-spawning coney. Heterogeneity and/or inferred barriers, based on
 microsatellites, involved St. Croix (red hind and coney) and the west
 coast of Puerto Rico (coney). Heterogeneity and/or inferred barriers,
 based on mitochondrial DNA, involved St. Croix (coney only). Genetic
 divergence in both species was stronger for microsatellites than for
 mitochondrial DNA, suggesting sex-biased dispersal in both species.
 Long-term migration rates, based on microsatellites, indicated asymmetric
 gene flow for both species in the same direction as mean surface currents
 in the region. Red hind had higher levels of variation in microsatellites
 and lower levels of variation in mitochondrial DNA. Long-term effective
 size and effective number of breeders were greater for red hind; estimates
 of θf a proxy for long-term effective female size, were the same in both
 species. Patterns of gene flow in both species appear to stem in part from
 shared aspects of larval and adult biology, local bathymetry, and surface
 current patterns. Differences in connectivity and levels of genetic
 variation between the species, however, likely stem from differences in
 behaviour related to reproductive strategy.
description: Microsatellite genotypes
 of red hind and coney
DOI: 10.5061/dryad.18796
title: Data from: The geography of divergence-with-gene-flow facilitates multi-trait adaptation and the evolution of pollinator isolation in Mimulus aurantiacus

description: Ecological adaptation is the driving force during
 divergence-with-gene-flow and generates reproductive isolation early in
 speciation. Although gene flow opposes divergence, local adaptation can be
 facilitated by factors that prevent the breakup of favorable allelic
 combinations. We investigated how selection, genetic architecture, and
 geography have contributed to the maintenance of floral trait divergence
 and pollinator isolation between parapatric ecotypes of Mimulus
 aurantiacus. Combining greenhouse, field, and genomic studies, we show
 that sharp clines in floral traits are maintained by spatially-varying
 selection. Although adaptation breaks down where the ecotypes co-occur,
 leading to the formation of a hybrid zone, the largely non-overlapping
 distributions of the ecotypes shield them from immigrant genes,
 facilitating divergence across most of the range. In contrast to the sharp
 genetic discontinuities observed across most hybrid zones, we observed a
 gradual cline in genome-wide divergence and a pattern of
 isolation-by-distance across the landscape. Thus, contrary to a long
 period of allopatry followed by recent re-contact, our data suggest that
 floral trait divergence in M. aurantiacus may have evolved with
 locally-restricted, but ongoing gene flow Therefore, our study reveals how
 the geographic distribution of an organism can contribute to the evolution
 of premating isolation in the early stages of divergence-with-gene-flow.
description: Raw floral trait data
 from the 16 common garden populationsThis MS excel file
 contains raw floral trait data for red ecotype, yellow ecotype and hybrid
 populations (Column A) of Mimulus aurantiacus raised in a common garden at
 the University of Oregon. Seeds were collected from 16 populations (column
 B) in the field and raised in a greenhouse. Each maternal line (column C)
 is represented by 2 seedlings (column D). We then measured 11 traits from
 2 flowers per plant (columns E - Z). All measurements are in mm, except
 for anthocyanin which is the absorbance at 520 nm.Raw floral trait
 data.xlsxFloral trait data used
 in the correlation and Principal Components analysesThis file contains
 phenotypic data for six floral traits (columns B to G) for 4 groups of
 plants (red ecotype (population UCSD), yellow ecotype (population LO), F1
 (red x yellow) and F2 (F1 x F1) grown in a common environment at the
 university of Oregon. All measurements are in mm, except for anthocyanin
 which is the absorbance at 520 nm.Data for correlation and PC
 analyses.xlsxField collected trait
 dataThis MS Excel file
 contains floral trait data collected from 8 natural populations (2 yellow
 ecotype populations: LO and POTR, 2 red ecotype populations: MT and UCSD,
 and 4 hybrid populations: WM, MW, OAK and LKW). All measurement are in mm
 except for anthocyanin absorbance which was measured at 520
 nm.
DOI: 10.5061/dryad.hf8qf
title: Data from: Stripes for warning and stripes for hiding: spatial frequency and detection distance

description: Striped patterns are common in nature and are used both as warning signals
 and camouflage. Their effectiveness in either role depends on their color
 and spatial frequency, and how these compare to the background. Although
 this general principle is well established, the specific detail of how
 visual texture influences defensive coloration remains untested in the
 field. For aposematic patterns, especially, little work has focused on how
 pattern components, as opposed to color, affect warning signal efficacy.
 By presenting artificial moth-like stimuli, pinned to tree bark, to wild
 avian predators, and human observers, we examine how the spatial frequency
 and orientation of stripes affects the survival and detectability of
 yellow-and-black (aversive) and olive-and-black (cryptic) patterns. For
 the cryptic stripes, we find that matching the dominant spatial frequency
 and orientation of the background increases survival against bird
 predation and decreases the distance from which humans first detect the
 target. For aversive stripes, however, survival against birds peaked at
 spatial frequencies that neither matched the dominant background spatial
 frequency nor maximized the mismatch between target and background. This
 peak in survival at intermediate spatial frequencies did not match
 detectability by humans: there was no difference in the initial detection
 distance between stripes of different spatial frequencies, although the
 distance at which stripes could be resolved did differ. We suggest that,
 although the best cryptic strategy is to match the dominant components of
 the background as closely as possible, the optimal aposematic signal is
 one that balances signal distinctiveness and recognition at a distance.
description: survivaldata_1ASurvival data from Experiment 1Asurvivaldata_1BSurvival data from Experiment 1BdetectiondataDetection and identification data from Experiment 2
DOI: 10.5061/dryad.t043g01
title: Data from: The last 50 years of climate-induced melting of the Maliy Aktru glacier (Altai Mountains, Russia) revealed in a primary ecological succession

description: In this article, we report and discuss the results obtained from a survey
 of plants, microorganisms (bacteria and fungi), and soil elements along a
 chronosequence in the first 600 m of the Maliy Aktru glacier's
 forefront (Altai Mountains, Russia). Many glaciers of the world show
 effects of climate change. Nonetheless, except for some local reports, the
 ecological effects of deglaciation have been poorly studied and have not
 been quantitatively assessed in the Altai Mountains. Here, we studied the
 ecological changes of plants, fungi, bacteria, and soil elements that take
 the form of a primary ecological succession and that took place over the
 deglaciated soil of the Maliy Aktru glacier during the last 50 year.
 According to our measurements, the glacier lost about 12 m per year during
 the last 50 years. Plant succession shows clear signs of changes along the
 incremental distance from the glacier forefront. The analysis of the plant
 α‐ and β‐diversity confirmed an expected increase of them with increasing
 distance from the glacier forefront. Moreover, the analysis of β‐diversity
 confirmed the hypothesis of the presence of three main stages of the plant
 succession: (a) initial (pioneer species) from 30 to 100 m; (b)
 intermediate (r‐selected species) from 110 to 120–150 m; and (c) final
 (K‐selected species) from 150 to 550. Our study also shows that
 saprotrophic communities of fungi are widely distributed in the glacier
 retreating area with higher relative abundances of saprotroph ascomycetes
 at early successional stages. The evolution of a primary succession is
 also evident for bacteria, soil elements, and CO2 emission and
 respiration. The development of biological communities and the variation
 in geochemical parameters represent an irrefutable proof that climate
 change is altering soils that have been long covered by ice.
description: Supplementary Table
 2Fungal metagenome and
 succession The metabarcoding libraries yielded 3,636,481 paired reads.
 After the removal of the low-quality sequences, chimaeras, non-target taxa
 (plants, Chromista, Protista, Protozoa, and Metazoa), and rare sequence
 types, we retained 1,305,772 sequences that following normalization were
 grouped in 855 operational taxonomic units (OTUs).
DOI: 10.5061/dryad.81k9m23
title: Data from: Phenotypic selection on floral traits in an urban landscape

description: Native species are increasingly living in urban landscapes associated with
 abiotic and biotic changes that may influence patterns of phenotypic
 selection. However, measures of selection in urban and non-urban
 environments, and exploration of the mechanisms associated with such
 changes, are uncommon. Plant-animal interactions have played a central
 role in the evolution of flowering plants and are sensitive to changes in
 the urban landscape, and thus provide opportunities to explore how urban
 environments modify selection. We evaluated patterns of phenotypic
 selection on floral and resistance traits of Gelsemium sempervirens in
 urban and non-urban sites. The urban landscape had increased florivory and
 decreased pollen receipt, but showed only modest differences in patterns
 of selection. Directional selection for one trait, larger floral display
 size, was stronger in urban compared to non-urban sites. Neither quadratic
 nor correlational selection significantly differed between urban and
 non-urban sites. Pollination was associated with selection for larger
 floral display size in urban compared to non-urban sites, due to
 differences in the translation of pollination into seeds rather than
 pollinator selectivity. Thus, our data suggest that urban landscapes may
 not result in sweeping differences in phenotypic selection but rather
 modest differences for some traits, potentially mediated by species
 interactions.
description: Gelsemium phenotypic
 selection dataThis data file contains
 floral and resistance traits, plant reproduction, pollination, nectar
 robbing, and florivory for plants from 16 sites (8 urban and 8
 non-urban).1 Gelsemium selection for
 Dryad.xlsx
DOI: 10.5061/dryad.5cs10
title: Data from: Frequency and fitness consequences of bacteriophage φ6 host range mutations

description: Viruses readily mutate and gain the ability to infect novel hosts, but few
 data are available regarding the number of possible host range-expanding
 mutations allowing infection of any given novel host, and the fitness
 consequences of these mutations on original and novel hosts. To gain
 insight into the process of host range expansion, we isolated and
 sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to
 infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found
 at least 17 unique suites of mutations among these 69 mutants. We assayed
 fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the
 standard laboratory host, P. phaseolicola. Mutants exhibited significantly
 lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola.
 Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P.
 phaseolicola compared to wildtype Φ6, confirming the prevalence of
 antagonistic pleiotropy during host range expansion. Further experiments
 revealed that the mechanistic basis of these fitness differences was
 likely variation in host attachment ability. In addition, using
 computational protein modeling, we show that host-range expanding
 mutations occurred in hotspots on the surface of the phage's host
 attachment protein opposite a putative hydrophobic anchoring domain.
description: Ford et al. Host Range
 Mutant DataData file contains
 fitness, plaque size, attachment rate and mutation frequency data for
 bacteriophage phi6 host range mutants that gained the ability to infect
 Pseudomonas pseudoalcaligenes ERA.