cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0h887
title: Data from: Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogen Rhynchosporium commune

description: To predict the response of plant pathogens to climate warming, data are
 needed on current thermal adaptation, the pathogen’s evolutionary
 potential and the link between them. We conducted a common garden
 experiment using isolates of the fungal pathogen Rhynchosporium commune
 from nine barley populations representing climatically diverse locations.
 Clonal replicates of 126 genetically distinct isolates were assessed for
 their growth rate at 12°C, 18°C and 22°C. Populations originating from
 climates with higher monthly temperature variation had higher growth rate
 at all three temperatures compared to populations from climates with less
 temperature fluctuation. Population differentiation in growth rate (Q_ST)
 was significantly higher at 22°C than population differentiation for
 neutral microsatellite loci (G_ST), consistent with local adaptation for
 growth at higher temperatures. At 18°C we found evidence for stabilizing
 selection for growth rate as Q_ST was significantly lower than G_ST.
 Heritability of growth rate under the three temperatures was substantial
 in all populations (0.58-0.76). Genetic variation was lower in populations
 with higher growth rate at the three temperatures and evolvability
 increased under heat stress in seven out of nine populations. Our findings
 imply that the distribution of this pathogen is unlikely to be genetically
 limited under climate warming, due to its high genetic variation and
 plasticity for thermal tolerance.
description: Raw data
 DryadGrowth rate data in
 mm/day for all temperatures, populations, isolates and
 replicates.
DOI: 10.15468/dl.9jzerw
title: Occurrence Download

description: A dataset containing 52 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 hondoensis"
 ]
}

 The dataset includes 52 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000801-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8mr63
title: Data from: Ecological character displacement between a native and an introduced species: the invasion of Anolis cristatellus in Dominica

description: Species invasions are a global scourge. Nonetheless, they provide the
 appropriate evolutionary setting to rigorously test the role that
 interspecific competition plays in species evolution. The process of
 ecological character displacement, in which species diverge in sympatry to
 minimize resource use overlap, is one example. Here, we examine whether
 ecological character displacement occurs as the result of a species
 invasion and, if so, whether morphological adaptations subsequently
 evolve. We studied the invasion of the lizard Anolis cristatellus in
 Dominica, where the native Anolis oculatus occurs, and compared nine
 allopatric and 11 sympatric populations at two scales: across the island,
 where A. cristatellus invaded since 1998, and in the northeastern region
 (Calibishie), where the species arrived in 2014. Perch height and
 diameter, as well as body, limb and toepad traits, were measured on 593
 adults. In sympatry, habitat divergence occurred rapidly but was
 associated with morphological divergence at the island scale only: A.
 oculatus perched higher and possessed shorter limbs, while A. cristatellus
 moved downward with associated longer limbs and, in females, fewer toepad
 lamellae. The different results for the two scales suggest that sympatry
 is too recent at Calibishie for morphological trait evolution to occur.
description: Table Dryad BJLS
 DufourMeasured hand and foot
 toepad traits (in mm2 table sheet 1 in Calibishie, 2 at the island scale);
 limb and body morphological traits (in mm, table sheet 3 in Calibishie, 2
 at the island scale) and ecological traits (in cm, table sheet 5 in
 Calibishie, 6 at the island scale).
DOI: 10.5061/dryad.8m11n
title: Data from: Ecological network inference from long-term presence-absence data

description: Ecological communities are characterized by complex networks of trophic
 and nontrophic interactions, which shape the dy-namics of the community.
 Machine learning and correlational methods are increasingly popular for
 inferring networks from co-occurrence and time series data, particularly
 in microbial systems. In this study, we test the suitability of these
 methods for inferring ecological interactions by constructing networks
 using Dynamic Bayesian Networks, Lasso regression, and Pear-son’s
 correlation coefficient, then comparing the model networks to empirical
 trophic and nontrophic webs in two ecological systems. We find that
 although each model significantly replicates the structure of at least one
 empirical network, no model significantly predicts network structure in
 both systems, and no model is clearly superior to the others. We also find
 that networks inferred for the Tatoosh intertidal match the nontrophic
 network much more closely than the trophic one, possibly due to the
 challenges of identifying trophic interactions from presence-absence data.
 Our findings suggest that although these methods hold some promise for
 ecological network inference, presence-absence data does not provide
 enough signal for models to consistently identify interactions, and
 networks inferred from these data should be interpreted with caution.
description: Food web adjacency list
 for France river datasetAdjacency list
 representing all feeding interactions for the France river dataset, as
 identified by a literature review of gut content analyses.
 'Parent' column represents the source of the interaction.
 'Child' column represents the target of the interaction.
 'Sign' represents the effect of the Parent species on the Child
 species. Since feeding interactions are +/-, each predator-prey pair will
 be represented by two rows: one for the negative effect of predator on
 prey, and one for the positive effect of prey on
 predator.Comte-adjlist.csvList of species for the France river network datasetComteSpNames-final.txtList of species for the Tatoosh middle intertidal datasettatoosh-control-exp-cv-spnames.txtPresence-Absence data for Tatoosh middle intertidalPresence-absence data for species in the Tatoosh middle intertidal (space-separated data frame). First column is a site identifier, second column is the census year, and all other columns are presence/absence for a species in a given site-year. Data for different sites are separated with a row of NAs.tatoosh-site-year-all.txtTrophic interaction adjacency list for Tatoosh data setOrganized as for the France adjacency list, but with trophic (feeding) interactions for the Tatoosh data set.tatoosh-trophic-adjlist.csvNontrophic interaction adjacency list for Tatoosh data setOrganized identically to the France adjacency list, but contains nontrophic (non-feeding) interactions for the Tatoosh data set.tatoosh-nontrophic-adjlist.csv
DOI: 10.5061/dryad.78521
title: Data from: Familial social structure and socially-driven genetic differentiation in Hawaiian short-finned pilot whales

description: Social structure can have a significant impact on divergence and evolution
 within species, especially in the marine environment, which has few
 environmental boundaries to dispersal. On the other hand, genetic
 structure can affect social structure in many species, through an
 individual preference toward associating with relatives. One social
 species, the short-finned pilot whale (Globicephala macrorhynchus), has
 been shown to live in stable social groups for periods of at least a
 decade. Using mitochondrial control sequences from 242 individuals and
 SNPs from 106 individuals, we examine population structure among
 geographic and social groups of short-finned pilot whales in the Hawaiian
 Islands, and test for links between social and genetic structure. Our
 results show that there are at least two geographic populations in the
 Hawaiian Islands: a Main Hawaiian Islands (MHI) population and a
 Northwestern Hawaiian Islands/Pelagic population (FST and ΦST P &lt;
 0.001), as well as an eastern MHI community and a western MHI community
 (FST P = 0.009). We find genetically-driven social structure, or high
 relatedness among social units and clusters (P &lt; 0.001), and a
 positive relationship between relatedness and association between
 individuals (P &lt; 0.0001). Further, socially-organized clusters are
 genetically distinct, indicating that social structure drives genetic
 divergence within the population, likely through restricted mate selection
 (FST P = 0.05). This genetic divergence among social groups can make the
 species less resilient to anthropogenic or ecological disturbance.
 Conservation of this species therefore depends on understanding links
 among social structure, genetic structure, and ecological variability
 within the species.
description: Ttru reference
 sequenceReference sequence for
 nuclear genome assembly from Tursiops truncatus.Supplemental File S1.
 Ttru_reference.fastaSNP
 genotypesLocation and variation
 data for nuclear SNPs used in this study.Supplemental Table S1. SNP
 genotypes.csv
DOI: 10.5061/dryad.2dh5n
title: Data from: Local and regional founder effects in lake zooplankton persist after thousands of years despite high dispersal potential

description: We reconstructed the genetic structure of a planktonic crustacean Daphnia
 longispina living in high mountain lakes and ponds in the Pyrenees to
 investigate whether it was shaped by persistent founder effects
 originating shortly after the last glacial maximum or by ongoing dispersal
 and effective migration (gene flow). We found that the genetic structure
 can largely be explained by a single colonization event following gradual
 deglaciation of the Pyrenees c. 10-15 000 years ago. Nuclear genetic
 diversity declined steeply from southeast to northwest, suggestive of
 serial colonization of available habitats with advancing deglaciation. The
 spatial genetic structure suggests that founder effects were major
 determinants of the present-day diversity, both at the catchment level and
 at the level of individual water bodies, further supporting extremely low
 effective migration rates. This study reveals a prime example of a founder
 effect that is both long-lasting and maintained at small spatial scales.
 Our data suggest a process of isolation by colonisation as a result of
 strong priority effects and monopolisation. We found evidence for the
 spread of haplotypes with Pyrenean ancestry across the Palearctic over
 distances up to 5500 km, although the local genetic structure after
 colonization was hardly influenced by contemporary dispersal. Finally, our
 data also suggest that mitochondrial mutation rates in the studied
 populations were seven times higher than typically assumed. Overall, we
 show that founder effects can persist for centuries even at small spatial
 scales at which the potential for dispersal is high.
description: Ventura-Microsats-PyreneesMicrosatellite genotyping results. Twenty five populations distributed at regional scale in the Eastern Pyrenees (Catalonia) were used for this analysis. Individual ID and sample location are shown.Ventura et al - Pyrenees- New Haplotypesfasta file showing the alignment of the partial sequence of the 12S mtDNA gene. Individual ID and correspondent GenBank accession number are shown
DOI: 10.5061/dryad.4s9m2
title: Data from: Nutritional geometry and fitness consequences in Drosophila suzukii, the Spotted-Wing Drosophila

description: Since its arrival to North America less than a decade ago, the invasive
 Spotted-Wing Drosophila (Drosophila suzukii) has inflicted substantial
 economic losses on soft fruit agriculture due to its ability to oviposit
 into ripening fruits. More effective management approaches for this
 species are needed, but little is known about the factors that influence
 behavioral choices made by D. suzukii when selecting hosts, or the
 consequences that their offspring experience when developing in different
 environments. Using a nutritional geometry methodology, we found that the
 ratio of proteins-to-carbohydrates (P:C) present in media greatly
 influenced adult D. suzukii behavior and subsequent offspring development.
 Whereas adult flies showed a strong bias in their oviposition and
 association behaviors toward carbohydrate-rich foods, larval survival and
 eclosion rate were strongly dependent on protein availability. Here, we
 explore the preference–performance hypothesis (PPH), in which females are
 predicted to oviposit on medias that provide the greatest offspring
 benefits, in regard to its relevance in D. suzukii behavior and
 consequences for management. Our results provide valuable insight into the
 ecology and evolution of this species that may hopefully lead to more
 effective management strategies.
description: FLYPOSITIONThis describes the total number of times in which a male or female D. suzukii was observed on the surface of one of eight different media inside an assay chamber.EGGS_CHOICE_STACKEDThis file includes the number of eggs that were laid on each of 8 different medias within an assay chamber.EGGS_NO_CHOICE_STACKEDNumber of eggs laid by individual D. suzukii females housed on one of eight different media typesFly_weightsDry weights of males and females D. suzukii collected from eight different media types.T_plus_SurvivalEgg to adult survivorship of D. suzukii raised on eight different media types (that contained antimicrobials, T+ assay)T_minus_SurvivalEgg to adult survivorship of D. suzukii raised on eight different media types (that did not contain antimicrobials, T- assay)T_plus_DevelopmentDate of ecolosion from pupae of adult D. suzukii raised on eight different media types (that contained antimicrobials, T+ assay)T_minus_DevelopmentDate of ecolosion from pupae of adult D. suzukii raised on eight different media types (that did not contain antimicrobials, T+ assay)
DOI: 10.5061/dryad.tb58947
title: Data from: Within-individual variation in sexual displays: signal or noise?

description: Animal sexual displays are typically repeated over time and consist of
 components that are also repeated within a display, creating potential for
 within-individual variation in signal production. Across taxa, patterns of
 variation in and female preferences for temporal properties of signals are
 well documented, but data describing how within-individual variation
 functions in communication are scarce. Is within-individual variation
 itself a signal of male quality, or noise that obscures another signal
 encoded by a temporal pattern? In this study of Cope’s gray treefrog, Hyla
 chrysoscelis, we used synthetic advertisement calls to examine the
 function of within-individual variation in two signal traits: pulse rate,
 a signal of species identity, and call rate, a signal of male quality. We
 examined relationships between male body condition and coefficients of
 variation within males for both signal traits. We then measured female
 preferences for within-individual variation. Because treefrogs communicate
 in noisy social aggregations, we repeated the experiment in quiet and at
 three amplitudes of chorus-shaped noise to evaluate how within-individual
 variation affects mate choice in natural settings. Within-individual
 variation in signal production was not predicted by male condition and
 likely acts as noise in this communication system. Females strongly
 discriminated against highly variable call rates, but not pulse rates,
 when the mean trait values of signals were taken into account. At its
 highest level, chorus noise abolished this effect, suggesting female
 preferences against within-individual variation are unlikely to be
 expressed in dense social aggregations.
description: Data from phonotaxis
 experimentsThese are data from
 phonotaxis experiments, including testing conditions, female responses,
 and post hoc calculations of experienced stimulus parameters based on the
 response latency from each trial. Please see the README file for more
 information.Hch_Variability_Discrimination_BehEco_data.csv
DOI: 10.5061/dryad.93553v8
title: Data from: Revisiting niche fundamentals with Tukey depth

description: The first attempts to describe species ecological niches were simple
 geometric procedures that depict the niche boundaries directly from
 environmental data. The convex hull was one of such procedures, popular
 for its simplicity, clear ecological rational and precise definition of
 the niche. However, it lacked the ability to differentiate areas of the
 niche with different probabilities of occurrence according to
 environmental suitability. We incorporate the Tukey depth, a mathematical
 tool to measure the centrality of a point within a cloud of points on a
 multidimensional space, in the convex hull approach to (i) propose a new
 procedure (CH‐Tukey) to estimate species’ environmental suitability, and
 (ii) estimate niche overlap coherently. In addition to a clear ecological
 rational and simplicity the CH‐Tukey procedure has a number of attractive
 features: use of presence‐only data; independence from background data;
 invariance to scale; robustness to outliers; and the decomposition of the
 niche into a finite number of iso‐suitability levels, permitting the
 computation of consistent overlap indices. We illustrate the use of
 CH‐Tukey, using occurrence data of the main Quercus species and subspecies
 from Western Mediterranean Europe, comparing its outputs with BIOCLIM and
 MaxEnt. Results showed distinct niche geometries among the different
 approaches. BIOCLIM produced rectilinear niches reflecting the assumption
 that ecological variables are independent in their action on the species.
 CH‐Tukey, relaxing this assumption, adjusts niche outer boundary and the
 inner suitability levels to the known occurrences. MaxEnt produced
 unbounded niche geometries, showing abrupt shifts in the species response
 to the environmental variables. The niche predictions obtained with
 geometric approaches, BIOCLIM and CH‐Tukey, are simpler but better aligned
 with Hutchinson's niche concept than those obtained with MaxEnt, this
 latter showing ecologically implausible relationships with the
 environmental variables. CH‐Tukey and the related overlap measures provide
 an adequate tool to explore niche properties and species–environment
 relationships.
description: Quercus_dataThis table contains the geographical coordinates (in the Iberian Peninsula) and four environmental variables (bio3=isothermality, bio6=minimum temperature of coldest month, bio12=annual precipitation and bio17=precipitation of driest quarter) for each occurrence of the six Quercus taxa modelled in our work (Qrob = Quercus robur, Qpyr = Quercus pyrenaica, Qbro = Q. faginea subsp. broteroi, Qfag = Q. faginea subsp. faginea, Qsub = Q. suber, Qrot = Q. rotundifolia). Original occurrence data were obtained from the Proyecto Anthos (http://www.anthos.es) and from the Herbarium “João de Carvalho e Vasconcellos” (Lisbon, LISI).
DOI: 10.5061/dryad.f2p64
title: Data from: Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements

description: The cladistic literature does not always specify the kind of multistate
 character treatment that is applied for an analysis. Characters can be
 treated either as unordered transformation series or as rooted [three-item
 analysis (3ia)] or unrooted state trees (ordered characters). We aimed to
 measure the impact of these character treatments on phylogenetic
 inference. Discrete characters can be represented either as rows or
 columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the
 present study, we use simulated and empirical examples to assess the
 relative merits of each method considering both the character treatment
 and representation. We measure two parameters (resolving power and
 artefactual resolution) using a new tree comparison metric, ITRI
 (inter-tree retention index). Our results suggest that the hierarchical
 character representation not only results (with our simulation settings)
 in the greatest resolving power, but also in the highest artefactual
 resolution. Our empirical examples provide equivocal results. Parsimony
 unordered states yield less resolving power and more artefactual
 resolutions than parsimony ordered states, both with our simulated and
 empirical data. Relationships between three operational taxonomic units
 (OTUs), irrespective of their relationships with other OTUs, are called
 three-item statements (3is). We compare the intersection tree (which
 reconstructs a single tree from all of the common 3is of source trees)
 with the traditional strict consensus and show that the intersection tree
 retains more of the information contained in the source trees.
description: Grand et al. SOM
 1100
 matrices with 8 taxa and 6 characters. These were used in our simulations
 to test the performance of several methods.Grand et al. SOM
 2Gadiform data matrix for
 parsimony analysis and character state order
 descriptions.Grand et al. SOM
 3Character data of
 gadiforms for 3ia.Grand et al. SOM
 4Character matrix of
 monilophytes for parsimony analyses with ordered or unordered
 characters.Grand et al. SOM
 5Character data of
 monilophytes for 3ia.Grand et al. SOM
 6Resolving power and
 artifactual resolution rate of the methods (parsimony with unordered and
 ordered states, and 3ia). Detailed table giving the results for each
 individual matrix.
DOI: 10.15468/dl.3edpvm
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Grevea eggelingii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 145 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000802-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.