cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.27900
title: Data from: Functional connectivity experiments reflect routine movement behavior of a tropical hummingbird species

description: Translocation experiments, in which researchers displace animals then
 monitor their movements to return home, are commonly used as tools to
 assess functional connectivity of fragmented landscapes. Such experiments
 are purported to have important advantages of being time efficient and
 standardizing 'motivation' to move across individuals. Yet, we
 lack tests of whether movement behavior of translocated birds reflects
 natural behavior of unmanipulated birds. We compared the routine movement
 behavior of a tropical hummingbird (Phaethornis guy) to that of
 experimentally translocated individuals. We tested for differences in
 site-selection patterns during movement at two spatial scales (point and
 path levels). We also compared movement rates between treatments.
 Behaviors documented during translocation experiments reflected those
 observed during routine movements. At the point level, both translocated
 and non-translocated birds showed similar levels of preference for mature
 tropical forest. At the path level, step selection functions showed both
 translocated and non-translocated hummingbirds avoiding movement across
 non-forested matrix and selecting streams as movement corridors. Movement
 rates were generally higher during translocation experiments. However, the
 negative influence of forest cover on movement rates was proportionately
 similar in translocation and routine movement treatments. We report the
 first evidence showing that movement behavior of birds during
 translocation experiments is similar to their natural movement behavior.
 Therefore, translocation experiments may be reliable tools to address
 effects of landscape structure on animal movement. We observed consistent
 selection of landscape elements between translocated and non-translocated
 birds, indicating that both routine and translocation movement studies
 lead to similar conclusions regarding the effect of landscape structure
 and forest composition on functional connectivity. Our observations that
 hummingbirds avoid non-forest matrix and select riparian corridors also
 provides a potential mechanism for pollen limitation in fragmented
 tropical forest.
description: Green Hermit location
 points 2008-2012Radio-telemetry location
 points recorded in 2008 and 2012. See README.txt for details on
 columns.Volpe et al Functional
 connectivity_dataset.xlsxPython code used to
 generate data to run the Step Selection FunctionThis python code allows
 the user to obtain the information needed to run a Step Selection
 Function. It generates random movements steps based on the frequency
 distribution of observed step lengths and turning angles, and calculates
 the following characteristics along those movement steps: proportion of
 different habitat types within user-defined buffers, habitat types at
 start and end points, number of gaps crossed, length of the step that
 takes place inside each habitat type and distance to a given
 feature.SSFdata.zip
DOI: 10.5061/dryad.6fj11j00
title: Data from: Genetic variation and evolution of secondary compounds in native and introduced populations of the invasive plant Melaleuca quinquenervia

description: We examined multivariate evolution of 20 leaf terpenoids in the invasive
 plant Melaleuca quinquenervia in a common garden experiment. While most
 compounds, including 1,8-Cineole and Viridiflorol, were reduced in home
 compared with invaded range genotypes, consistent with an evolutionary
 decrease in defense, one compound (E-Nerolidol) was greater in invaded
 than home range genotypes. Nerolidol was negatively genetically correlated
 with Cineole and Viridiflorol, and the increase in this compound in the
 new range may have been driven by this negative correlation. There was
 positive selection on all three focal compounds, and a loss of genetic
 variation in introduced range genotypes. Selection skewers analysis
 predicted an increase in Cineole and Viridiflorol and a decrease or no
 change in Nerolidol, in direct contrast to the observed changes in the new
 range. This discrepancy could be due to differences in patterns of
 selection, genetic correlations or the herbivore communities in the home
 versus introduced ranges. While evolutionary changes in most compounds
 were consistent with the Evolution of Increased Competitive Ability
 Hypothesis, changes in other compounds as well as selection patterns were
 not, indicating that it is important to understand selection and the
 nature of genetic correlations to predict evolutionary change in invasive
 species.
description: dryad
 archive
DOI: 10.5061/dryad.t1rv6
title: Data from: Species wood density and the location of planted seedlings drive early-stage seedling survival during tropical forest restoration

description: 1.The success of restoration projects is known to vary widely, with
 outcomes relating to numerous biotic and abiotic factors. Though many
 studies have examined the factors associated with long-term restoration
 success, few have examined which factors impact the establishment of
 restoration plantings. 2.In Australia's Wet Tropics, we used a large
 replicated restoration experiment to assess seedling survival for 24
 native rainforest species commonly used in local restoration efforts. The
 experiment allowed for a rigorous assessment of the effects of species
 functional traits, planting conditions and landscape and local scale
 biotic and abiotic factors on seedling survival. This study reports on
 seedling survival between three different time periods of 0 – 4, 4 – 9 and
 9 – 31 months post planting. 3.The probability of seedling survival was
 influenced by multiple factors, varying in importance over time. Across
 the whole study period, seedlings with high wood density and which were
 planted closer to intact forest consistently displayed the highest
 probabilities of survival. Transient factors affecting seedling survival
 across the three time periods included plot aspect (0 – 4 months only),
 the identity of the planter and slope (4 – 9 and 9 – 31 months). Overall,
 species survival did not differ between the low (6 species) and high (24
 species) diversity treatments, but was significantly lower in monocultures
 of Flindersia brayleyana by the end of the study. 4.We demonstrate that
 early-stage seedling survival depends on species wood density and planting
 location. Our results support the use of species with more conservative
 growth strategies when limited funds are available for follow-up
 plantings. Specifically, high wood density species had significantly
 higher survival than lower wood density, early successional species
 typically used in rainforest restoration plantings. 5.Synthesis and
 applications. Our study highlights the importance of wood density and
 landscape structure to the initial survival of rainforest plantings.
 Factors influencing seedling survival shifted over time, but most
 importantly, our results highlight that, when planting into abandoned
 pastures, it may be preferable to select species with higher wood
 densities to maximize survival during the crucial early stages of
 establishment and growth.
description: Seedling mortality data
 from restoration plantingsData of seedling
 mortality for 24 endemic Australian rainforest species within a replicated
 restoration planting experiment over three years. Data also contains
 topographical data (slope, aspect, distance from
 forest).Charles_et_al_data_JAPPL-2017-00852.csvSpecies trait dataTrait data for species used in restoration experiment. Data includes: Wood density, seed mass, maximum adult height, successional stage, dispersal vectorCharles_et_al_trait_data_JAPPL-2017-00852.csv
DOI: 10.5061/dryad.5874v7h
title: Data from: Functional responses of aquatic and riparian vegetation to hydrogeomorphic restoration of channelized lowland streams and their valleys

description: 1. Streams and riparian zones are highly heterogeneous ecosystems. Their
 high biodiversity is promoted by variable flow velocities and water
 depths, strong hydrological gradients and disturbance regimes. However,
 human interventions like damming and channelization have degraded these
 ecosystems worldwide. And, although restoration efforts have increased in
 the past decades, ecological improvement is lagging. 2. We assessed
 vegetation development in channelized lowland stream valleys in the
 Netherlands, combining innovative restoration measures to the stream and
 stream valleys. This ‘stream valley restoration’ entailed construction of
 narrower and shallower channels to increase flow velocities during base
 discharges, meandering of the watercourse to increase flow and depth
 heterogeneity and excavation of banks to create wide v-shaped stream
 valleys. We evaluated the effects on functional aspects of the developing
 in-stream and riparian vegetation by comparing restored stream reaches to
 nearby unrestored reaches. 3. The reduced channel dimensions led to higher
 flow velocities, which, through interaction with meandering, triggered a
 higher variability in flow and depth. Combined with enlargement of the
 floodplain, this promoted flooding in stream valleys and created wider
 environmental gradients. Plant diversity strongly increased in the
 floodplain area, the land-water interface and the shallow water habitat at
 the channel margins, but decreased in the central parts of stream
 channels. There, higher flow velocities led to more typically lotic
 (running water) in-stream plant communities, indicated by a sharp decrease
 in floating-leaved species and an increase in trailing species. Riparian
 vegetation showed a higher beta-diversity across the wider valley slopes
 of restored reaches, with more wetland species in areas with water tables
 between 0.0 and -0.6 m, and more upland species as well. 4. Synthesis and
 applications. This study demonstrates that the combination of strongly
 reduced channel dimensions, remeandering and widening of riparian zones,
 is effective in restoring in-stream and riparian habitat heterogeneity.
 The restoration efforts lead to distinct immediate increases in total and
 beta-diversity of many typical stream and riparian plant species. Overall,
 this stresses the importance of applying restoration measures to both
 streams and stream valleys simultaneously, considering them as a single
 landscape unit. 27-Nov-2018
description: Fraaije et al 2018
 JAPPLEight worksheets with
 data on physicochemical variables and on aquatic and riparian vegetation
 in restored and nearby unrestored reaches of channelized lowland streams
 in the Netherlands, with description of column headers (worksheet 1), data
 on abiotic variables of riparian zones (worksheets 2 and 3), data on
 abiotic variables of the in-stream habitat (worksheets 4, 5 and 6), and
 data on plant species percent cover per plot (worksheets 7 and
 8).
DOI: 10.5061/dryad.cg32n
title: Data from: Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent

description: The origin of the fungal wheat pathogen Phaeosphaeria nodorum remains
 unclear despite earlier intensive global population genetic and
 phylogeographical studies. We sequenced 1,683 bp distributed across three
 loci in 355 globally distributed Phaeosphaeria isolates, including 74
 collected in Iran near the center of origin of wheat. We identified nine
 phylogenetically distinct clades, including two previously unknown species
 tentatively named P1 and P2 collected in Iran. Coalescent analysis
 indicates that P1 and P2 are sister species of P. nodorum and the other
 Phaeosphaeria species identified in our analysis. Two species, P. nodorum
 and P. avenaria f. sp. tritici 1 (Pat1), comprised ∼85% of the sampled
 isolates, making them the dominant wheat-infecting pathogens within the
 species complex. We designed a PCR-RFLP assay to distinguish P. nodorum
 from Pat1. Approximately 4% of P. nodorum and Pat1 isolates showed
 evidence of hybridization. Measures of private allelic richness at SSR and
 sequence loci suggest that the center of origin of P. nodorum coincides
 with its host in the Fertile Crescent. We hypothesize that the origin of
 this species complex is also in the Fertile Crescent, with four species
 out of nine found exclusively in the Iranian collections.
description: Coalescent Tree Model
 for Phaeospaheria spp. ComplexThis is a ready to
 execute XML file generated in Beauti that will run in the program *BEAST.
 It contains the full dataset, including all isolates and 3 separate loci
 for the referenced paper. Isolates are grouped into taxa according to
 species classification. This grouping allows the TMRCA to be estimated for
 specific taxa or groups of taxa.All_isolates_GTRNucmodels.xml
DOI: 10.5061/dryad.33th6
title: Data from: Gradual loading ameliorates maladaptation in computational simulations of vein graft growth and remodelling

description: Vein graft failure is a prevalent problem in vascular surgeries, including
 bypass grafting and arteriovenous fistula procedures in which veins are
 subjected to severe changes in pressure and flow. Animal and clinical
 studies provide significant insight, but understanding the complex
 underlying coupled mechanisms can be advanced using computational models.
 Towards this end, we propose a new model of venous growth and remodelling
 (G&R) based on a constrained mixture theory. First, we identify
 constitutive relations and parameters that enable venous adaptations to
 moderate perturbations in haemodynamics. We then fix these relations and
 parameters, and subject the vein to a range of combined loads (pressure
 and flow), from moderate to severe, and identify plausible mechanisms of
 adaptation versus maladaptation. We also explore the beneficial effects of
 gradual increases in load on adaptation. A gradual change in flow over 3
 days plus an initial step change in pressure results in fewer
 maladaptations compared with step changes in both flow and pressure, or
 even a gradual change in pressure and flow over 3 days. A gradual change
 in flow and pressure over 8 days also enabled a successful venous
 adaptation for loads as severe as the arterial loads. Optimization is used
 to accelerate parameter estimation and the proposed framework is general
 enough to provide a good starting point for parameter estimations in
 G&R simulations.
description: Data related to results
 from the paper.zip contains data
 related to several figures in the paper.GnR_vein_RSIF_data.zip
DOI: 10.5061/dryad.8976q
title: Data from: Genetic dissection of adaptive form and function in rapidly-speciating cichlid fishes

description: Genes of major phenotypic effects and strong genetic correlations can
 facilitate adaptation, direct selective responses and potentially lead to
 phenotypic convergence. However, the preponderance of this type of genetic
 architecture in repeatedly-evolved adaptations remains unknown. Using
 hybrids between Haplochromis chilotes (thick-lipped) and H. nyererei
 (thin-lipped) we investigated the genetics underlying hypertrophied lips
 and elongated heads, traits that evolved repeatedly in cichlids. At least
 25 loci of small-to-moderate and mainly additive effects were detected.
 Phenotypic variation in lip and head morphology was largely independent.
 Although several QTL overlapped for lip and head morphology traits, they
 were often of opposite effects. The distribution of effect signs suggests
 strong selection on lips. The fitness implications of several detected
 loci were demonstrated using a laboratory assay testing for the
 association between genotype and variation in foraging performance. The
 persistence of low fitness alleles in head morphology appears to be
 maintained through antagonistic pleiotropy/close linkage with
 positive-effect lip morphology alleles. Rather than being based on few
 major loci with strong positive genetic correlations, our results indicate
 that the evolution of the Lake Victoria thick-lipped ecomorph is the
 result of selection on numerous loci distributed throughout the genome.
description: Genotypic
 DataHenning_et_al_Evolution_2017_geno_file.csvPhenotypic DataHenning_et_al_Evolution_2017_pheno_file.csv
DOI: 10.5061/dryad.712
title: Data from: Mammalian metabolic allometry: do intraspecific variation, phylogeny, and regression models matter?

description: Power scaling relationships between body mass and organismal traits are
 fundamental to biology. Compilations of mammalian masses and basal
 metabolic rates date back over a century and are used both to support and
 to assail the universal quarter‐power scaling invoked by the metabolic
 theory of ecology. However, the slope of this interspecific allometry is
 typically estimated without accounting for intraspecific variation in body
 mass or phylogenetic constraints on metabolism. We returned to the
 original literature and culled nearly all unique measurements of body mass
 and basal metabolism for 695 mammal species and (1) phylogenetically
 corrected the data using the fullest available phylogeny, (2) applied
 several different regression analyses, (3) resampled regressions by
 drawing randomly selected species from each of the polytomies in the
 phylogenetic hypothesis at each iteration, and (4) ran these same analyses
 independently on separate clades. Overall, 95% confidence intervals of
 slope estimates frequently did not include 0.75, and clade‐specific slopes
 varied from 0.5 to 0.85, depending on the clade and regression model. Our
 approach reveals that the choice of analytical model has a systematic
 influence on the estimated allometry, but irrespective of the model
 applied, we find little support for a universal metabolic rate–body mass
 scaling relationship.
description: Mammal body mass and BMR
 measurementsSiegOnlineAppendixA.pdfSiegAmNat2009_AppendixA.xls
DOI: 10.5061/dryad.3jt35
title: Data from: Sectional relationships in the Eurasian bearded iris (subgen. Iris) based on phylogenetic analyses of sequence data

description: Subgenus Iris is wholly Eurasian, distributed in temperate regions from
 northeastern China to eastern and southern Europe where they occur in
 mountainous and/or dry rocky sites from near sea level to elevations of
 4,500 m. These species have an easily discerned synapomorphy, a
 multicellular beard on each petaloid sepal. Currently two large and
 relatively well known and four smaller and less known sections are
 recognized in the subgenus. This study investigated the monophyly of
 circumscribed sections and relationships among these sections. Seventy-one
 taxa, representing each of the six sections and about 80% of the
 recognized species in subgen. Iris, and 11 outgroup taxa were included in
 the study. Also included were five Asian species that share some
 morphological characteristics with subgen. Iris but are typically
 considered in other subgenera. Phylogenetic analyses of sequence data
 recovered six major clades but sects. Psammiris, Pseudoregelia, and
 Regelia, are not monophyletic as currently circumscribed. The sister clade
 to subgen. Iris is comprised of I. domestica and I. dichotoma, two
 beardless species that occur in eastern Asia. Iris verna, a species from
 the eastern United States is sister to I. domestica + I. dichotoma +
 subgen. Iris. The sepal of I. verna has pubescence but not a beard of
 multicellular trichomes.
description: SubgenIrisPlast
 DatasetSubgenIrisPlast is an
 aligned dataset of seven plastid markers comprising almost 8,000 sequenced
 bp for 87 Iris taxa. Seventy-one taxa, representing each of the six
 sections and about 80% of the recognized species in subgenus Iris, and 11
 outgroup taxa were included in the study. Also included were five Asian
 species that share some morphological characteristics with subgenus Iris
 but are typically considered in other subgenera. This dataset is utilized
 in the publication: Wilson, C. 2017. Sectional relationships in the
 Eurasian bearded Iris (subgen. Iris) based on phylogenetic analyses of
 sequence data. Syst. Bot.
DOI: 10.5061/dryad.t2m75
title: Data from: Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

description: Because novel environmental conditions alter the selection pressure on
 genes or entire subgenomes, adaptive and nonadaptive changes will leave a
 measurable signature in the genomes, shaping their molecular evolution. We
 present herein a model of the trajectory of plastid genome evolution under
 progressively relaxed functional constraints during the transition from
 autotrophy to a nonphotosynthetic parasitic lifestyle. We show that
 relaxed purifying selection in all plastid genes is linked to obligate
 parasitism, characterized by the parasite’s dependence on a host to
 fulfill its life cycle, rather than the loss of photosynthesis.
 Evolutionary rates and selection pressure coevolve with macrostructural
 and microstructural changes, the extent of functional reduction, and the
 establishment of the obligate parasitic lifestyle. Inferred bursts of gene
 losses coincide with periods of relaxed selection, which are followed by
 phases of intensified selection and rate deceleration in the retained
 functional complexes. Our findings suggest that the transition to obligate
 parasitism relaxes functional constraints on plastid genes in a stepwise
 manner. During the functional reduction process, the elevation of
 evolutionary rates reaches several new rate equilibria, possibly relating
 to the modified protein turnover rates in heterotrophic plastids.
description: Dataset
 S1Annotation details and
 presence/absence list of plastid genesDataset_S1.xlsxDataset_S2Results of the relative rate tests (dN)Dataset_S3Results of relative rate tests (dS)Dataset_S4Results from functional complex-wise tests for relaxation of selection strength and lifestyle effectsDataset_S5Reconstruction of the ancestral states of all plastid genes and functional complexesDataset_S6Results of phylogenetic principal component analysisDataset_S7Phylogenetic principal regression using MCMC-GLMMDataset_S8Indel frequency as length variation per gene per species relative to the average length of the respective intact geneDataset_S9Model-ranked results of Monte Carlo Markov chain coupled generalized linear mixed models with cumulative BIC weightsDataset_S10Model-ranked results of Monte Carlo Markov chain coupled generalized linear mixed model statistics of models with a cumulative BIC-weight of at least 0.8HBL/Perl/R scriptsExample scripts (HyPhy batch language, perl) for analysing evolutionary rates and indels; R scripts for producing heatmaps from relative rate data and reconstructing the indel history over a given phylogeny after indel-coding with SeqState; includes five example data and tree files.scripts_for_rates_and_indel_analysis.zip