cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r69g1
title: Data from: Invasion genetics of the Bermuda buttercup (Oxalis pes-caprae): complex intercontinental patterns of genetic diversity, polyploidy and heterostyly characterize both native and introduced populations.

description: Genetic diversity in populations of invasive species is influenced by a
 variety of factors including reproductive systems, ploidy level,
 stochastic forces associated with colonization and multiple introductions
 followed by admixture. Here, we compare genetic variation in native and
 introduced populations of the clonal plant Oxalis pes-caprae to
 investigate the influence of reproductive mode and ploidy on levels of
 diversity. This species is a tristylous geophyte native to South Africa.
 Invasive populations throughout much of the introduced range are composed
 of a sterile clonal pentaploid short-styled form. We examined morph
 ratios, ploidy level, reproductive mode and genetic diversity at nuclear
 microsatellite loci in 10 and 12 populations from South Africa and the
 Western Mediterranean region, respectively. Flow cytometry confirmed
 earlier reports of diploids and tetraploids in the native range, with a
 single population containing pentaploid individuals. Introduced
 populations were composed mainly of pentaploids, but sexual tetraploids
 were also found. There was clear genetic differentiation between ploidy
 levels, but sexual populations from both regions were not significantly
 different in levels of diversity. Invasive populations of the pentaploid
 exhibited dramatically reduced levels of diversity but were not
 genetically uniform. The occurrence of mixed ploidy levels and stylar
 polymorphism in the introduced range is consistent with multiple
 introductions to the Western Mediterranean. This inference was supported
 by variation patterns at microsatellite loci. Our study indicates that
 some invasive populations of Oxalis pes-caprae are not entirely clonal, as
 often assumed, and multiple introductions and recombination have the
 potential to increase genetic variation in the introduced range.
description: Oxalis_pes-caprae_SSRRange, population, individual code, morph and ploidy level, together with microsatellite data for Oxalis pes-caprae individuals. Columns are separated by TABs. Due to the polyploid constitution of these taxa, multiple alleles per individual and locus were scored.Oxalis_pes-caprae_FCMPloidy level of Oxalis pes-caprae populations investigated in this study. The sample size, genome size estimates (in pg) using flow cytometry and minimum (Min) and maximum (Max) genome size estimates are provided for each population and ploidy level (2x, diploid; 4x, tetraploid; 5x, pentaploid).Oxalis pes-caprae neighbor-joining treeTree output from a neighbor-joining distance analysis based on dissimilarity matrix of 380 individuals of Oxalis pes-caprae and seven SSR markers. The format is a nexus tree file format and the analyses were carried in the package 'ape' (Paradis et al. 2004) in R.Oxalis pes-caprae_njtree_nex
DOI: 10.5061/dryad.2sj7q
title: Data from: The effect of meal frequency in a reduced-energy regimen on the gastrointestinal and appetite hormones in patients with type 2 diabetes: a randomised crossover study

description: Background: Appetite and gastrointestinal hormones (GIHs) participate in
 energy homeostasis, feeding behavior and regulation of body weight. We
 demonstrated previously the superior effect of a hypocaloric diet regimen
 with lower meal frequency (B2) on body weight, hepatic fat content,
 insulin sensitivity and feelings of hunger compared to the same diet
 divided into six smaller meals a day (A6).Studies with isoenergetic diet
 regimens indicate that lower meal frequency should also have an effect on
 fasting and postprandial responses of GIHs.The aim of this secondary
 analysis was to explore the effect of two hypocaloric diet regimens on
 fasting levels of appetite and GIHs and on their postprandial responses
 after a standard meal. It was hypothesized that lower meal frequency in a
 reduced-energy regimen leading to greater body weight reduction and
 reduced hunger would be associated with decreased plasma concentrations of
 GIHs: gastric inhibitory peptide (GIP), glucagon-like peptide-1(GLP-1),
 peptide YY(PYY), pancreatic polypeptide (PP) and leptin and increased
 plasma concentration of ghrelin. The postprandial response of satiety
 hormones (GLP-1, PYY and PP) and postprandial suppression of ghrelin will
 be improved. Methods: In a randomized crossover study, 54 patients
 suffering from type 2 diabetes (T2D) underwent both regimens.The
 concentrations of GLP-1, GIP, PP, PYY, amylin, leptin and ghrelin were
 determined using multiplex immunoanalyses. Results: Fasting leptin and GIP
 decreased in response to both regimens with no difference between the
 treatments (p=0.37 and p=0.83, respectively). Fasting ghrelin decreased in
 A6 and increased in B2 (with difference between regimens p=0.023). Fasting
 PP increased in B2with no significant difference between regimens
 (p=0.17). Neither GLP-1 nor PYY did change in either regimen. The decrease
 in body weight correlated negatively with changes in fasting ghrelin
 (r=-0.4, p&lt;0.043) and the postprandial reduction of ghrelin
 correlated positively with its fasting level (r=0.9, p&lt;0.001). The
 postprandial responses of GIHs and appetite hormones were similar after
 both diet regimens. Conclusions: Both hypocaloric diet regimens reduced
 fasting leptin and GIP and postprandial response of GIP comparably. The
 postprandial responses of GIHs and appetite hormones were similar after
 both diet regimens. Eating only breakfast and lunch increased fasting
 plasma ghrelin more than the same caloric restriction split into six
 meals. The changes in fasting ghrelin correlated negatively with the
 decrease in body weight. These results suggest that for type 2 diabetic
 patients on a hypocaloric diet, eating larger breakfast and lunch may be
 more efficient than six smaller meals during the day.
description: DatasetDATASET.xlsx
DOI: 10.5061/dryad.r7490
title: Data from: Ecomorphological convergence in planktivorous surgeonfishes

description: Morphological convergence plays a central role in the study of evolution.
 Often induced by shared ecological specialization, homoplasy hints at
 underlying selective pressures and adaptive constraints that
 deterministically shape the diversification of life. Though midwater
 zooplanktivory has arisen in adult surgeonfishes (family Acanthuridae) at
 least four independent times, it represents a clearly specialized state,
 requiring the capacity to swiftly swim in midwater locating and sucking
 small prey items. While this diet has commonly been associated with
 specific functional adaptations in fishes, acanthurids present an
 interesting case study as all other species feed by grazing on benthic
 algae and detritus, requiring a vastly different functional morphology
 that emphasizes biting behaviors. We examined the feeding morphology in 30
 acanthurid species and, combined with a pre-existing phylogenetic tree,
 compared the fit of evolutionary models across two diet regimes:
 zooplanktivores and non-zooplanktivorous grazers. Accounting for
 phylogenetic relationships, the best-fitting model indicates that
 zooplanktivorous species are converging on a separate adaptive peak from
 their grazing relatives. Driving this bimodal landscape, zooplanktivorous
 acanthurids tend to develop a slender body, reduced facial features,
 smaller teeth, and weakened jaw adductor muscles. However, despite these
 phenotypic changes, model fitting suggests that lineages have not yet
 reached the adaptive peak associated with plankton feeding even though
 some transitions appear to be over 10 million years old. These findings
 demonstrate that the selective demands of pelagic feeding promote
 repeated—albeit very gradual—ecomorphological convergence within
 surgeonfishes, while allowing local divergences between closely related
 species, contributing to the overall diversity of the clade.
description: Morphometric
 dataEntire morphometric
 dataset collected from surgeonfish specimens.AcanthData2.xlsxAcanthuridTreeNexus file for the phylogenetic tree used in this study (modified from Sorenson et al., 2013).
DOI: 10.5061/dryad.9pg3r
title: Data from: On the complexity of triggering evolutionary radiations

description: Recent developments in phylogenetic methods have made it possible to
 reconstruct evolutionary radiations from extant taxa, but identifying the
 triggers of radiations is still problematic. Here, we propose a conceptual
 framework to explore the role of variables that may impact radiations. We
 classify the variables into extrinsic conditions vs intrinsic traits,
 whether they provide background conditions, trigger the radiation, or
 modulate the radiation. We used three clades representing angiosperm
 phylogenetic and structural diversity (Ericaceae, Fagales and Poales) as
 test groups. We located radiation events, selected variables potentially
 associated with diversification, and inferred the temporal sequences of
 evolution. We found 13 shifts in diversification regimes in the three
 clades. We classified the associated variables, and determined whether
 they originated before the relevant radiation (backgrounds), originated
 simultaneously with the radiations (triggers), or evolved later
 (modulators). By applying this conceptual framework, we establish that
 radiations require both extrinsic conditions and intrinsic traits, but
 that the sequence of these is not important. We also show that
 diversification drivers can be detected by being more variable within a
 radiation than conserved traits that only allow occupation of a new
 habitat. This framework facilitates exploration of the causative factors
 of evolutionary radiations.
description: Maximum Clade
 Credibility Tree of PoalesMCC_POALES.treMaximum Clade Credibility Tree of FagalesMCC_FAGALESMaximum Clade Credibility Tree of EricaceaeMCC_Ericaceae.tre
DOI: 10.5061/dryad.cg7d4
title: Data from: Isolation-driven functional assembly of plant communities on islands

description: The physical and biotic environment is often considered the primary driver
 of functional variation in plant communities. Here, we examine the
 hypothesis that spatial isolation may also be an important driver of
 functional variation in plant communities where disturbance and dispersal
 limitation may prevent species from occupying all suitable habitats. To
 test this hypothesis, we surveyed the vascular plant composition of 30
 islands in the Gulf of Maine, USA, and used available functional trait and
 growth form data to quantify the functional composition of these islands.
 We categorized species based on dispersal mode and used a landscape metric
 of isolation to assess the potential role of dispersal limitation as a
 mechanism of isolation-driven assembly. We tested for island and species
 level effects on functional composition using a hierarchical Bayesian
 framework to better assess the causal link between isolation and
 functional variation. Growth form composition and the community mean value
 of functional traits related to growth rate, stress tolerance, and
 nutrient use varied significantly with island isolation. Functional traits
 and growth forms were significantly associated with dispersal mode, and
 spatial isolation was the strongest driver of primary trait variation,
 while island properties associated with environmental drivers in our
 system were not strong predictors of trait variation. Despite the
 species-level association of dispersal mode and functional traits,
 dispersal mode only accounted for a small proportion of the overall
 isolation effect on community-level trait variation. Our study suggests
 that spatial isolation can be a key driver of functional assembly in plant
 communities on islands, though the role of particular dispersal processes
 remains unclear.
description: Island species lists and
 island propertiesFirst sheet is an
 island-species matrix of species presences (0 or 1). Second sheet includes
 spatial data for each island. Taxonomic nomenclature follows Haines
 (2011). See associated publication for details on data collection methods
 and supplemental appendix for additional metadata.Maine Island
 Data.xlsx
DOI: 10.5061/dryad.nc69n
title: Data from: Changes in soil microbial communities due to biological invasions can reduce allelopathic effects

description: Summary 1. Soil microbes are important in mediating allelopathic
 interactions between invasive and native plants in the field. However, it
 was not known how these interactions vary in the process of biological
 invasions and the effects of soil microbes. Knowing these may facilitate
 understanding dynamics and mechanisms of biological invasions and managing
 invaded ecosystems. 2. We conducted competition and seed germination
 experiments to determine the allelopathic effects of Ageratina adenophora
 in soils from 42 sites with varying abundances of the invasive plant. Then
 we isolated the microbes that had the ability to degrade the
 allelochemicals of the invasive plant and tested their functions. 3. In
 both experiments, the allelopathic effects of the invasive plant were much
 stronger in soils from non-invaded sites than in soils from invaded sites.
 Activities of the allelochemical-degrading microbes were higher and
 degradation of the allelochemicals of the invasive plant was faster in
 soils from invaded sites than in soils from non-invaded sites. In living
 soils from 30 sites with increasing abundance of A. adenophora, the
 allelopathic effects of the invasive plant decreased and degradation of
 the allelochemicals and activity of the allelochemical-degrading microbes
 gradually increased. 4. Two bacterial strains were isolated from the
 soils. Inoculation of Arthrobacter sp. ZS, which was isolated from soil
 invaded by A. adenophora, greatly increased the degradation of the
 allelochemicals, thereby decreasing its allelopathic effects. 5. Synthesis
 and applications. Our results indicate that soils may accumulate microbes
 that are able to degrade allelochemicals in the process of biological
 invasions, gradually reducing the allelopathic effects of invasive
 species. It is necessary to consider the effects of soil microbes when
 studying dynamics and mechanisms of biological invasions. Application of
 allelochemical-degrading microbes may facilitate ecological restoration of
 invaded or newly disturbed ecosystems by alleviating allelopathic
 inhibition of invasive plants on native plants.12-Jan-2017
description: DATA from three
 experimentsdata-lyp.xlsx
DOI: 10.5061/dryad.9k2k7
title: Data from: Temporal modelling of ballast water discharge and ship-mediated invasion risk to Australia

description: Biological invasions have the potential to cause extensive ecological and
 economic damage. Maritime trade facilitates biological invasions by
 transferring species in ballast water, and on ships' hulls. With
 volumes of maritime trade increasing globally, efforts to prevent these
 biological invasions are of significant importance. Both the International
 Maritime Organization and the Australian government have developed policy
 seeking to reduce the risk of these invasions. In this study, we
 constructed models for the transfer of ballast water into Australian
 waters, based on historic ballast survey data. We used these models to
 hindcast ballast water discharge over all vessels that arrived in
 Australian waters between 1999 and 2012. We used models for propagule
 survival to compare the risk of ballast-mediated propagule transport
 between ecoregions. We found that total annual ballast discharge volume
 into Australia more than doubled over the study period, with the vast
 majority of ballast water discharge and propagule pressure associated with
 bulk carrier traffic. As such, the ecoregions suffering the greatest risk
 are those associated with the export of mining commodities. As global
 marine trade continues to increase, effective monitoring and biosecurity
 policy will remain necessary to combat the risk of future marine invasion
 events.
description: routes_dataContains a list of the number of voyages (into Australia) between each pair of marine ecoregions, by year and vessel type.
DOI: 10.5061/dryad.jm090
title: Data from: Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe

description: Wild boar (Sus scrofa), one of the most widespread wildlife species, has
 entered a stage of continuous growth in Europe, and could even be
 considered a pest species. We analysed microsatellite variability in 723
 wild boars from across Europe, including the northern Dinaric Balkans. Our
 aims were: (1) to define the population structure of wild boars in the
 Balkans and its relation with other European populations; (2) to estimate
 effective populations sizes, levels of intra- and inter-population
 diversity, inbreeding migration and gene flow patterns; (3) to test
 subpopulations for bottlenecks; (4) to interpret these results in light of
 current knowledge about the demographic history of wild boars in Europe;
 and (5) to discuss the relevance of these findings for management and
 conservation. Strong population structuring was observed and 14
 subpopulations were revealed. High genetic diversity was found, and
 besides the well-known identity of the Italian populations of Sardinia and
 Castelporziano, we bring new insights to other potential relevant,
 refugial populations such as Littoral Slovenia, South Portugal,
 North-western Iberia, and a whole entire cluster in the Balkans. There was
 evidence of gene flow going from these refugial subpopulations towards
 less peripheral and more admixed subpopulations. Recent population
 bottlenecks and expansions were detected, mostly in the peninsular refuge
 subpopulations. The results are consistent with the fluctuations of wild
 boar numbers in Europe since the beginning of the twentieth century. These
 results should be taken into account in future conservation and management
 plans for wild boar populations in Europe.
description: Wild boar
 microsatellites genotypesInclude original
 genotypes for 11 microsatellites analyzed in wild boars from the Balkans,
 Iberia, Italy and Central-eastern Europe.Velickovic et
 al_microsatellites genotypes_for
 dryad.xlsx
DOI: 10.5061/dryad.544b1
title: Data from: Warning signals are seductive: relative contributions of color and pattern to predator avoidance and mate attraction in Heliconius butterflies

description: Visual signaling in animals can serve many uses, including predator
 deterrence and mate attraction. In many cases, signals used to advertise
 unprofitability to predators are also used for intraspecific
 communication. Although aposematism and mate choice are significant forces
 driving the evolution of many animal phenotypes, the interplay between
 relevant visual signals remains little explored. Here, we address this
 question in the aposematic passion-vine butterfly Heliconius erato by
 using color- and pattern-manipulated models to test the contributions of
 different visual features to both mate choice and warning coloration. We
 found that the relative effectiveness of a model at escaping predation was
 correlated with its effectiveness at inducing mating behavior, and in both
 cases wing color was more predictive of presumptive fitness benefits than
 wing pattern. Overall, however, a combination of the natural (local) color
 and pattern was most successful for both predator deterrence and mate
 attraction. By exploring the relative contributions of color versus
 pattern composition in predation and mate preference studies, we have
 shown how both natural and sexual selection may work in parallel to drive
 the evolution of specific animal color patterns.
description: Predation
 dataData indicate the number
 of predation attempts by birds on four different artificial butterfly
 model types: a local type, color-switched type, achromatic type, and
 non-local type.Mate preference
 dataData indicate the number
 of approaches (sheet 1) and courtship attempts (sheet 2) by male
 Heliconius erato butterflies directed toward artificial butterfly models
 of four types: a local type, color-switched type, achromatic type, and
 non-local type.
DOI: 10.5061/dryad.1771t
title: Data from: Resampling method for applying density-dependent habitat selection theory to wildlife surveys

description: Isodar theory can be used to evaluate fitness consequences of
 density-dependent habitat selection by animals. A typical habitat isodar
 is a regression curve plotting competitor densities in two adjacent
 habitats when individual fitness is equal. Despite the increasing use of
 habitat isodars, their application remains largely limited to areas
 composed of pairs of adjacent habitats that are defined a priori. We
 developed a resampling method that uses data from wildlife surveys to
 build isodars in heterogeneous landscapes without having to predefine
 habitat types. The method consists in randomly placing blocks over the
 survey area and dividing those blocks in two adjacent sub-blocks of the
 same size. Animal abundance is then estimated within the two sub-blocks.
 This process is done 100 times. Different functional forms of isodars can
 be investigated by relating animal abundance and differences in habitat
 features between sub-blocks. We applied this method to abundance data of
 raccoons and striped skunks, two of the main hosts of rabies virus in
 North America. Habitat selection by raccoons and striped skunks depended
 on both conspecific abundance and the difference in landscape composition
 and structure between sub-blocks. When conspecific abundance was low,
 raccoons and striped skunks favored areas with relatively high proportions
 of forests and anthropogenic features, respectively. Under high
 conspecific abundance, however, both species preferred areas with rather
 large corn-forest edge densities and corn field proportions. Based on
 random sampling techniques, we provide a robust method that is applicable
 to a broad range of species, including medium- to large-sized mammals with
 high mobility. The method is sufficiently flexible to incorporate multiple
 environmental covariates that can reflect key requirements of the focal
 species. We thus illustrate how isodar theory can be used with wildlife
 surveys to assess density-dependent habitat selection over large
 geographic extents.
description: Capture data of raccoons
 and striped skunks in Montérégie and Estrie regionsCapture data of raccoons
 and striped skunks during wildlife surveys in Montérégie and Estrie
 regions, Québec, Canada. These data were used to illustrate the resampling
 method in the case study. The columns “X_METER” and “Y_METER” are X and Y
 projected coordinates (in meters) of live-trap locations. The locations
 were projected into UTM Zone 18N coordinates with NAD 1983
 datum.Capture_data_Tardy_et_al.xlsx