cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84fq2vh
title: Data from: Shifts in phenological distributions reshape interaction potential in natural communities

description: Climate change has changed the phenologies of species worldwide, but it
 remains unclear how these phenological changes will affect species
 interactions and the structure of natural communities. Using a novel
 approach to analyse long‐term data of 66 amphibian species pairs across
 eight communities, we demonstrate that phenological shifts can
 significantly alter the interaction potential of coexisting competitors.
 Importantly, these changes in interaction potential were mediated by
 non‐uniform, species‐specific shifts in entire phenological distributions
 and consequently could not be captured by metrics traditionally used to
 quantify phenological shifts. Ultimately, these non‐uniform shifts in
 phenological distributions increased the interaction potential for 25% of
 species pairs (and did not reduce interaction potential for any species
 pair), altering temporal community structure and potentially increasing
 interspecific competition. These results demonstrate the potential of
 phenological shifts to reshape temporal structure of natural communities,
 emphasising the importance of considering entire phenological
 distributions of natural populations.
description: FrogCallsNETexasDaily frog & toad calling data (12 species) for 8 NE Texas sites from 2001-2015dailycalls_dryad.xlsx
DOI: 10.5061/dryad.7b90m0b
title: Data from: Context-dependent induction of allelopathy in plants under competition

description: Some plants use allelopathy to compete against neighbouring plants, and
 the ability to induce allelopathic compound production in response to
 competition is hypothesized to be adaptive, as plants can save costs of
 metabolite production in the absence of competitors. However, whether
 plants induce allelopathy has rarely been explored so far. We studied the
 inducibility of polyacetylenes—putative allelopathic compounds in Solidago
 altissima—in response to competition. Polyacetylenes were found in natural
 soil surrounding S. altissima patches within the range of concentration
 known to inhibit competitor growth. Individual S. altissima plants with
 higher polyacetylene concentration in roots suppressed the growth of the
 competitor plants more, suggesting that root polyacetylene levels
 proximate plants’ allelopathic capacity. Competition induced
 polyacetylenes in a context-dependent manner: Whereas introduced Japanese
 and Australian populations of S. altissima had higher constitutive
 concentration of polyacetylenes than the native North American
 populations, inducibility was observed only in Australian plants, where
 the population is still at an early stage of invasion. Also, induction
 became more prominent under nutrient depletion, where enhanced allelopathy
 may be particularly beneficial for suppressing a competitor’s exploitative
 capacity. Finally, we found weak evidence for a trade-off between
 constitutive and induced polyacetylenes. The observed patterns suggest
 that allelopathic plants could respond to competition by inducing
 allelochemical production, but the benefit of such plasticity may vary
 across time and space. Shifts in competitor communities in introduced
 range over time may shape plant’s plastic responses to competition, while
 variation in resource availability may alter competitive environment to
 influence the degree to which plants induce allelopathy.
description: Uesugi_etal_dataSecondary metabolite data for experiments conducted in 2010, 2015, & 2016.
DOI: 10.5061/dryad.0p32m6c
title: Data from: Experiments with artificial nests provide evidence for ant community stratification and nest site limitation in a tropical forest

description: Ants are dominant in tropical forests and many species nest in hollow
 cavities. The manner in which species are vertically stratified in these
 complex habitats is not known, with lack of nest sites being proposed to
 limit ant populations. Here we assess ant community stratification and
 nest site limitation in a lowland rainforest in New Guinea using
 experimental addition of artificial bamboo nests of two cavity sizes
 (small: ~12 mm. large: ~32 mm diameter) placed at ground level, in the
 understorey, and in the canopy. We also conducted a pilot experiment to
 test the utility of nest translocation. Nests were checked for occupancy
 after 10 weeks and half of the occupied nests were then translocated
 between forest plots, while keeping same vertical position. Occupancy of
 small nests was much higher in the understorey and canopy than at ground
 level (~75% versus ~25%). Translocation was successful, as a majority of
 nests was inhabited by the same species before and after translocation and
 there was no impact of translocation to a different plot compared to the
 control, except for a reduction in colony size at ground level. Our
 experiment demonstrates a vertical stratification in community composition
 of ants nesting in hollow dead cavities and shows that these ants are more
 nest-site limited in the higher strata than at ground level. Use of small
 artificial cavities has great potential for future experimental studies,
 especially for those focused on arboreal ants, as occupancy is high and
 translocation does not negatively affect their colony size.
description: Data from: Experiments
 with artificial nests provide evidence for ant community stratification
 and nest site limitation in a tropical forestThis file contains data
 from the experimental project from lowland forest Papua New Guinea. It
 contains 4 sheets: 1) Nest data with data about bamboo nests and ant
 colonies found in them. 2) TunaBaits data with information about
 communities of ants captured by tuna bait sampling in the same plots. 3)
 SpeciesCodes with Latin names of all ant species codes 4)
 NestPer400squareMeterEstimation with data from Wanang locality including
 estimation of a number of nests per 400m2.Mottl_Biotropica_data.xlsx
DOI: 10.5061/dryad.303k4j2
title: Data from: Spatially structured intraspecific trait variation can foster biodiversity in disturbed, heterogeneous environments

description: Trait variation within populations is an important area of research for
 empirical and theoretical ecologists. While differences between
 individuals are doubtlessly ubiquitous, their role for species coexistence
 is much less clear and highly debated. Both unstructured (random) and
 structured (linked to space, time or inheritance) intraspecific trait
 variation (ITV) may modify species interactions with nontrivial
 consequences for emerging community compositions. In many ecosystems,
 these compositions are further driven by prevalent disturbance regimes. I
 therefore explored the effects of unstructured as well as spatially
 structured ITV under disturbances in a generic ecological model of
 competing sessile species. Using spatially explicit, individual-based
 simulations, I studied how intraspecific variation in life history traits
 together with interspecific trade-offs and disturbance regimes shape
 long-term community composition. I found that (i) unstructured ITV does
 not affect species coexistence in the given context, (ii) spatially
 structured ITV may considerably increase coexistence, but (iii) spatially
 clumped disturbances reduce this effect of spatially structured ITV,
 especially if interspecific trade-offs involve dispersal distance. The
 findings suggest that spatially structured ITV with individual trait
 responses to local habitat conditions differing among species may create
 or expand humps in disturbance-diversity relationships. Hence, if present,
 these forms of spatially structured ITV should be included in ecological
 models and will be important for reliably assessing community responses to
 environmental heterogeneity and change.
description: Simulation data for
 manuscript 10.1111/oik.05787Simulation results. All
 details in readme.txt.data 10.1111
 oik.05787.zip
DOI: 10.5061/dryad.s97v921
title: Data from: Public-private partnership wetland restorations provide quality forage for waterfowl in Northern New York

description: The Partners for Fish and Wildlife Program and Wetlands Reserve Program
 are U.S. federal programs that provide financial and technical assistance
 to restore wetland habitats on private property, and are important tools
 for the conservation and management of waterfowl. This study examined
 whether these wetland restorations successfully restored one important
 component of waterfowl habitat, the availability of vegetative forage, at
 sites in the St. Lawrence River Valley of New York. We conducted surveys
 at 47 restored and 18 reference wetlands to characterize the vegetation
 assemblage in terms of its value as forage for waterfowl. Results suggest
 that these public-private partnership wetland restorations develop
 assemblages of wetland vegetation that are similar to reference wetlands.
 Vegetation assemblage metrics, including estimates of species richness,
 the richness of species of food value, the Vegetative Forage Quality
 Index, and the cover of species of food value did not differ between
 restored-reference wetland pairs. However, invasive species were common at
 sites, and we detected a negative association between the cover of
 invasive species at the Vegetative Forage Quality Index at both restored
 and reference wetlands. Based on these results, we conclude that Partners
 for Fish and Wildlife Program and Wetland Reserve Program wetland
 restorations provide quality forage for breeding and migratory waterfowl
 in this region, but that the presence of invasive vegetation at sites has
 the potential to decrease the quality of vegetative forage at sites over
 time.
description: Benson et al. 2019 Food
 Value Manuscript DataThe following file
 contains README information and raw data in support of this
 manuscript.Benson_et_al_2018_Food_Value_Manuscript_Data_S1.xlsx
DOI: 10.5281/zenodo.18391295
title: Data associated with "Surface energy driven crumpling transition in thin sheets"
DOI: 10.5061/dryad.655tf67
title: Data from: Finding a home in the noise: cross-modal impact of anthropogenic vibration on animal search behaviour

description: Chemical cues and signals enable animals to sense their surroundings over
 vast distances and find key resources, like food and shelter. However, the
 use of chemosensory information may be impaired in aquatic habitats by
 anthropogenic activities, which produce both water-borne sounds and
 substrate-borne vibrations, potentially affecting not only vibroacoustic
 sensing but other modalities as well. We attracted marine hermit crabs
 (Pagurus acadianus) in field experiments using a chemical cue indicative
 of a newly available shell home. We then quantified the number of crabs
 arriving in control versus impulsive noise conditions. Treatment (control
 or noise), time (before or after), and the interaction between the two
 significantly affected the numbers of crabs, with fewer crabs attracted to
 the chemical cue after noise exposure. The results indicate that noise can
 affect chemical information use in the marine environment, acting
 cross-modally to impact chemically-guided search behaviour in free-ranging
 animals. Broadly, anthropogenic noise and seabed vibration may have
 profound effects, even on behaviours mediated by other sensory modalities.
 Hence, the impact of noise should be investigated not only within, but
 also across sensory modalities.
description: Roberts and Laidre DRYAD
 data June 2019Results of the
 experiment, in terms of hermit crabs counted before or after a treatment
 (noise or control) are in the first sheet. The remaining sheets are the
 vibration measurements (m/s^-1) of the noise source, split by axis of
 motion.
DOI: 10.5281/zenodo.18391294
title: Data associated with "Surface energy driven crumpling transition in thin sheets"
DOI: 10.5061/dryad.89bv2s6
title: Data from: Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): new genomic tools for breeding programs and management of natural resources

description: The European flat oyster (Ostrea edulis) is a highly appreciated mollusk
 with an important aquaculture production throughout the 20th century, in
 addition to playing an important role on coastal ecosystems.
 Overexploitation of natural beds, habitat degradation, introduction of
 non-native species and epidemic outbreaks have severely affected this
 important resource, particularly, the protozoan parasite Bonamia ostreae,
 which is the main concern affecting its production and conservation. In
 order to identify genomic regions and markers potentially associated with
 bonamiosis resistance, six oyster beds distributed throughout the European
 Atlantic coast were sampled. Three of them have been exposed to this
 parasite since the early 1980’s and showed some degree of innate
 resistance (long-term affected group, LTA), while the other three were
 free of B. ostreae at least until sampling date (naïve group, NV). A total
 of 14,065 SNPs were analyzed, including 37 markers from candidate genes
 and 14,028 from a medium density SNP array. Gene diversity was similar
 between LTA and NV groups suggesting no genetic erosion due to long term
 exposure to the parasite, and three population clusters were detected
 using the whole dataset. Tests for divergent selection between NV and LTA
 groups detected the presence of a very consistent set of 22 markers,
 located within a putative single genomic region, which suggests the
 presence of a major quantitative trait locus associated with B. ostreae
 resistance. Moreover, 324 outlier loci associated with factors other than
 bonamiosis were identified allowing fully discrimination of all the oyster
 beds. A practical tool which included the 84 highest discriminative
 markers for tracing O. edulis populations was developed and tested with
 empirical data. Results reported herein could assist the production of
 stocks with improved resistance to bonamiosis, and facilitate the
 management of oyster beds for recovery production and ecosystem services
 provided by this species.
description: OyToTotGenepop input file including all the beds and markers used in the study (14,065 markers). Location codes are shown in Table 1 of the manuscript.Oy22Genepop input file with the 22 divergent outliers associated to bonamia resistance with the strict criterion (outliersPOOL-S). Location codes are shown in Table 1 of the manuscript.Oy87Genepop input file with the 87 divergent outliers associated to bonamia resistance with the less strict criterion (outliersPOOL-L). Location codes are shown in Table 1 of the manuscript.Oy324Genepop input file with the 324 divergent outliers detected in individual scenarios (outliersIND). Location codes are shown in Table 1 of the manuscript.Description of the files deposited in Dryad Vera et al 2019
DOI: 10.5061/dryad.2g8856k
title: Data from: Nongenetic paternal effects via seminal fluid

description: Mounting evidence suggests that nongenetic paternal effects on offspring
 may be widespread among animal taxa, but the mechanisms underlying this
 form of nongenetic inheritance are not yet fully understood. Here we show
 that seminal fluids underlie paternal effects on early offspring survival
 in an insect, the cricket Teleogryllus oceanicus, and quantify the
 contribution of this paternal effect to the inheritance of this important
 fitness trait. We used castrated males within a full-sib half-sib
 experimental design to show that seminal fluid donors were responsible for
 variation in the survival of developing embryos to hatching, and in their
 subsequent survival to adulthood. Increased expression of two seminal
 fluid protein genes, previously found to be positively associated with
 sperm quality, were found to be negatively associated with embryo
 survival. These nongenetic paternal effects hold important implications
 for the evolution of adaptive maternal responses to sperm competition, and
 more broadly for the interpretation of sire effects from classic
 quantitative genetic breeding designs.
description: Complete
 workbookSheet 1 contains
 survival data for embryos, sheet 2 survival probability from hatch to
 adulthood, sheet 3 the seminal fluid donor gene expression and their
 family mean embryo survival and whether adults were obtained, sheet 4
 female and sheet 5 male offspring phenotypesSimmons_EvolLet.xlsx
DOI: 10.5061/dryad.4j15t24
title: Data from: Post-glacial colonization of northern coastal habitat by bottlenose dolphins: a marine leading-edge expansion?

description: Oscillations in the Earth’s temperature and the subsequent retreating and
 advancing of ice-sheets around the polar regions are thought to have
 played an important role in shaping the distribution and genetic
 structuring of contemporary high-latitude populations. After the Last
 Glacial Maximum (LGM), retreating of the ice-sheets would have enabled
 early colonizers to rapidly occupy suitable niches to the exclusion of
 other conspecifics, thereby reducing genetic diversity at the
 leading-edge. Bottlenose dolphins (genus Tursiops) form distinct coastal
 and pelagic ecotypes, with finer scale genetic structuring observed within
 each ecotype. We reconstruct the post-glacial colonization of the
 Northeast Atlantic (NEA) by bottlenose dolphins using habitat modelling
 and phylogenetics. The AquaMaps model hindcasted suitable habitat for the
 LGM in the Atlantic lower latitude waters and parts of the Mediterranean
 Sea. The time-calibrated phylogeny, constructed with 86 complete
 mitochondrial genomes including 30 generated for this study and created
 using a multi-species coalescent model, suggests that the expansion to the
 available coastal habitat in the NEA happened via founder events starting
 ~15,000 years ago (95% highest posterior density interval: 4,900–26,400).
 The founders of the two distinct coastal NEA populations comprised as few
 as two maternal lineages that originated from the pelagic population. The
 low effective population size and genetic diversity estimated for the
 shared ancestral coastal population subsequent to divergence from the
 pelagic source population are consistent with leading-edge expansion.
 These findings highlight the legacy of the Late Pleistocene glacial cycles
 on the genetic structuring and diversity of contemporary populations.
description: Delphinids_SABD1_SA99_gene_regions_concatenatedAlignment FASTA-file of concatenated mtDNA genes of 18 delphinids and two Tursiops spp.Tursiops_gene_regions_concatenatedAlignment FASTA-file of concatenated mtDNA genes of 86 Tursiops spp.Tursiops_Steno_bredanensis_aligned_whole_mtDNAFASTA-alignment file of whole mtDNA Tursiops spp. and Steno bredanensisBEAST2_Delphinid_Strict_clock_3rd_codonsBEAST2 xml file to run a strict clock model with delphinids using 3rd codon positions of mtDNA genesStarBEAST2_Tursiops_input_3rd_codonsStarBEAST2 xml file to run a strict clock model with Tursiops spp. using 3rd codon positions of mtDNA genes
DOI: 10.5061/dryad.n445r0h
title: Data from: Assortative mating in animals and its role for speciation

description: Evolutionary theory predicts that assortative mating – the tendency of
 similar individuals to mate with each other – plays a key role for
 speciation by generating reproductive isolation between diverging
 populations. However, comprehensive tests for an effect of assortative
 mating on species richness at the macro-evolutionary scale are lacking. We
 used a meta-analytic approach to test the hypothesis that the strength of
 assortative mating is positively related to species richness across a
 broad range of animal taxa. Specifically, we ran a phylogenetically
 independent meta-analysis using an extensive database of 1447 effect sizes
 for the strength of assortative mating measured within populations,
 encompassing 307 species from 130 families and 14 classes. Our results
 suggest that there is no relationship between the strength of assortative
 mating and species richness across and within major taxonomic groups and
 trait categories. Moreover, our analysis confirms an earlier finding that
 animals typically mate assortatively (global effect size r = 0.36; 95%
 confidence limits: 0.19 − 0.52) when accounting for phylogenetic
 non-independence. In conclusion, we argue that future advances will rely
 on a better understanding of the evolutionary causes and consequences of
 the observed intra- and interspecific variation in the strength of
 assortative mating.
description: Raw Data
 FileData file containing all
 raw effect sizes (Pearson correlation coefficients r) included in this
 meta-analysis.Janicke_et_al_DATA_raw.xlsxData file of family mean estimatesData file containing mean effect sizes (Pearson correlation coefficients r) for each taxonomic family together with estimates of species richness and crown age.Janicke_et_al_DATA_byFamily.xlsxList of primary studiesFull reference list of primary studies included in this meta-analysis.Janicke_et_al_RefPrimaryStudies.docxPhylogenyPhylogeny in NEWICK format used to control for phylogenetic non-independence.Janicke_et_al_PHYLOGENY.txt
DOI: 10.5061/dryad.r5d94c8
title: Data from: Climate outweighs native vs. non-native range-effects for genetics and common garden performance of a cosmopolitan weed

description: Comparing genetic diversity, genetic differentiation and performance
 between native and non-native populations has advanced our knowledge of
 contemporary evolution and its ecological consequences. However, such
 between-range comparisons can be complicated by high among-population
 variation within native and non-native ranges. For example, native vs.
 non-native comparisons between small and non-representative subsets of
 populations for species with very large distributions have the potential
 to mislead because they may not sufficiently account for within-range
 adaptation to climatic conditions, and demographic history that may lead
 to non-adaptive evolution. We used the cosmopolitan weed Conyza canadensis
 to study the interplay of adaptive and demographic processes across, to
 our knowledge, the broadest climatic gradient yet investigated in this
 context. To examine the distribution of genetic diversity, we genotyped 26
 native and 26 non-native populations at 12 microsatellite loci.
 Furthermore, we recorded performance traits for 12 native and 13
 non-native populations in the field and in the common garden. To analyze
 how performance was related to range and/or climate, we fit pedigree
 mixed-effects models. These models weighed the population random effect
 for co-ancestry to account for the influence of demographic history on
 phenotypic among-population differentiation. Genetic diversity was very
 low, selfing rates were very high, and both were comparable between native
 and non-native ranges. Non-native populations out-performed native
 populations in the field. However, our most salient result was that both
 neutral genetic differentiation and common garden performance were far
 more correlated with the climatic conditions from which populations
 originated than native vs. non-native range-affiliation. Including
 co-ancestry of our populations in our models greatly increased explained
 variance and our ability to detect significant main effects for
 among-population variation in performance. High propagule pressure and
 high selfing rates, in concert with the ability to adapt rapidly to
 climatic gradients, may have facilitated the global success of this weed.
 Neither native nor non-native populations were homogeneous groups but
 responded comparably to similar environments in each range. We suggest
 that studies of contemporary evolution should consider widely distributed
 and genotyped populations to disentangle native vs. non-native
 range-effects from varying adaptive processes within ranges and from
 potentially confounding effects of demographic history.
description: data_SPAGeDi_formatThe microsatellite data is presented in a format that is accepted by the software SPAGeDi. You may use SPAGeDi to re-run the analyses and/or to convert the data into other formats.