cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h388h3g
title: Data from: Predation risk shaped by habitat and landscape complexity in urban environments

description: 1. Habitat loss and modification are hallmarks of anthropogenic
 ecosystems, but the consequences for ecosystem functions and services
 often remain unclear. Understanding these links in cities is complicated
 by strong but fine-scale differences in habitat structure among green
 space patches, and a high variance in habitat amount across urban
 landscapes. 2. We used airborne laser scanning (ALS) data to disentangle
 the effects of 3D woody habitat heterogeneity of urban home gardens, and
 woody habitat amount at four landscape spatial scales (50, 100, 250, 500
 m), on the predation risk of artificial sentinel prey by birds and
 arthropods. 3. In both predator groups, and at all the investigated
 spatial scales, cross-scale interactive effects between garden habitat
 heterogeneity and habitat amount in the urban landscape were the main
 drivers of predation. Risk of bird predation by birds was highest in
 heterogeneous garden habitats, but only in densely built urban landscapes
 where habitat amount was low to intermediate (10-20%) at large spatial
 scales (250-500 m). It dropped independently of garden habitat
 heterogeneity when habitat amount became too low (&lt;10%) at small
 (50-100 m) spatial scales. In contrast, risk of predation by arthropods
 mostly peaked in homogenous garden habitats when habitat amount was
 intermediate (20%) at large spatial scales. 4. Our findings show that the
 ability of urban green space patches to sustain ecosystem functions in
 cities mainly depends on cross-scale interactive effects with larger-scale
 habitat amount. In birds, predation risk can increase when high
 patch-scale habitat heterogeneity contrasts with reduced larger-scale
 habitat amount, suggesting concentration effects. Yet thresholds exist
 under which ecosystem functioning drops independently of habitat
 structure. 5. Synthesis and applications. The potential of small-scale
 interventions to enhance habitat heterogeneity (e.g. by planting native
 trees with understory shrubs) for restoring ecosystem functions such as
 bird predation in urban areas is dependent on wider landscape habitat
 structure. Urban planning should therefore adopt a multi-scale approach to
 sustain and restore ecosystem functions and services; a simple but still
 not broadly recognized finding. Airborne laser scanning is a useful tool
 to infer habitat structure across a hierarchy of scales in spatially
 heterogeneous anthropogenic ecosystems.
description: Response variables and
 experimental treatmentThe presence or absence
 of predator attack marks on the caterpillar models and experimental
 treatment data for each caterpillar.20180523_Frey_et_al_JApplEcol2018_predation_events_and_experimental_treatment.txtLaser scan dataAirborne laser scanning (ALS) data of 3D woody habitat heterogeneity of urban home gardens, and woody habitat amount at four landscape spatial scales (50, 100, 250, 500 m).20180523_Frey_et_al_JApplEcol2018_ALS_habitat_amount_and_heterogeneity_measures.txt
DOI: 10.5061/dryad.0rh0t
title: Data from: Population genetic dynamics of an invasion reconstructed from the sediment egg bank

description: Biological invasions are a global issue with far-reaching consequences for
 single species, communities and whole ecosystems. Our understanding of
 modes and mechanisms of biological invasions requires knowledge of the
 genetic processes associated with successful invasions. In many instances,
 this information is particularly difficult to obtain as the initial phases
 of the invasion process often pass unnoticed and we rely on inferences
 from contemporary population genetic data. Here, we combined historic
 information with the genetic analysis of resting eggs to reconstruct the
 invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s
 from the resting egg bank in the sediments. We identified the invader as
 ‘European D. pulicaria’ originating from meso- and eutrophic lowland lakes
 and ponds in Central Europe. The founding population was characterized by
 extremely low genetic variation in the resting egg bank that increased
 considerably over time. Furthermore, strong evidence for selfing and/or
 biparental inbreeding was found during the initial phase of the invasion,
 followed by a drop of selfing rate to low levels in subsequent decades.
 Moreover, the increase in genetic variation was most pronounced during
 early stages of the invasion, suggesting additional introductions during
 this period. Our study highlights that genetic data covering the entire
 invasion process from its beginning can be crucial to accurately
 reconstruct the invasion history of a species. We show that propagule
 banks can preserve such information enabling the study of population
 genetic dynamics and sources of genetic variation in successful invasive
 populations.
description: Sample information and
 analysis codesMicrosatellite
 genotypes, sample IDs, age model data, sequence alignments, tree files,
 hatching data, STRUCTURE input files and R codes for sliding windows
 analyses and pairwise DST and FST calculationsData files and R
 codes.zip
DOI: 10.5061/dryad.2n5h6
title: Data from: The genetic signature of range expansion in a disease vector - the black-legged tick

description: Monitoring and predicting the spread of emerging infectious diseases
 requires that we understand the mechanisms of range expansion by its
 vectors. Here, we examined spatial and temporal variation of genetic
 structure among 13 populations of the Lyme disease vector, the
 black-legged tick, in southern Quebec, where this tick species is
 currently expanding and Lyme disease is emerging. Our objective was to
 identify the primary mode of tick movement into Canada based on observed
 spatial and temporal genetic patterns. Upon genotyping ten microsatellite
 loci from 613 tick specimens, we found multiple genetic signatures of
 frequent long-distance dispersal events, supporting the hypothesis that
 migratory birds are the primary carriers of black-legged ticks into
 southern Quebec. When we compared results from analyses of pairwise
 differences among ticks collected from eight different sites at different
 years between 2011 and 2014, we found that genetic variation observed
 among tick individuals appeared to be better explained by collection year
 than sampling locality. This suggests that while cohorts of black-legged
 ticks can rapidly invade large areas across southern Quebec, they also
 appear to be undergoing frequent turnover. Finally, the amount of genetic
 variation in tick populations across our study area appeared to be related
 to their degree of establishment, with established populations displaying
 a lower amount of temporal genetic variation than adventitious ones. Given
 that Lyme disease infection risk in a region can be influenced by the
 relative presence of established and/or adventitious tick populations, our
 results are useful for understanding both the seasonality and spatial
 variation of Lyme disease.
description: Leo et al_JH_Electronic
 Supplementary MaterialFINAL_Leo et al_JH_Electronic
 Supplementary Material 2.xlsx
DOI: 10.15468/dl.xjn2yq
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lycianthes fasciculata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 140 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000944-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q0032
title: Data from: Ecological causes and consequences of flower color polymorphism in a self-pollinating plant (Boechera stricta)

description: Intraspecific variation in flower color is often attributed to
 pollinator-mediated selection, yet this mechanism cannot explain flower
 color polymorphisms in self-pollinating species. Indirect selection
 mediated via biotic and abiotic stresses could maintain flower color
 variation in these systems. The selfing forb, Boechera stricta, typically
 displays white flowers, but some individuals produce purple flowers. We
 quantified environmental correlates of flower color in natural
 populations. To disentangle plasticity from genotypic variation, we
 performed a multiyear field experiment in five gardens. In controlled
 conditions, we evaluated herbivore preferences and the effects of drought
 stress and soil pH on flower color expression. In natural populations,
 purple-flowered individuals experienced lower foliar herbivory than did
 their white-flowered counterparts. This pattern also held in the common
 gardens. Additionally, low-elevation environments induced pigmented
 flowers (plasticity), and the likelihood of floral pigmentation decreased
 with source elevation of maternal families (genetic cline). Viability
 selection favored families with pigmented flowers. In the laboratory,
 herbivores exerted greater damage on tissue derived from white- vs
 purple-flowered individuals. Furthermore, drought induced pigmentation in
 white-flowered lineages, and white-flowered plants had a fecundity
 advantage in the well-watered control. Flower color variation in selfing
 species is probably maintained by herbivory, drought stress, and other
 abiotic factors that vary spatially.
description: natural_populations_individualThis file contains data from transects in natural populations on individual plants. This dataset supports the section on the methods and results called "Environmental correlates of flower color variation"natural_populations_plotThis file contains the data to analyze the environmental correlates of flower color variation. The results are laid out in the text (Environmental correlates of flower color variation) and Table S3.common_gardenThis file contains the data for family-level analyses of the common garden experiment.no_choice_experimentThis file contains the data for the no choice experimentchoice_experimentThis file contains the data for the choice experiment.greenhouse_experimentThis file contains data from the greenhouse experiment.
DOI: 10.5061/dryad.k8bt6
title: Data from: Phylogenetic systematics of Cochlospermaceae (Malvales) based on molecular and morphological evidence

description: Cochlospermaceae (Malvales) is a small family of two genera, Amoreuxia and
 Cochlospermum. Cochlospermum has a pantropical distribution with species
 present in Mexico, Central and South America, the West Indies, Africa,
 India, Southeast Asia, and northern Australia, whereas Amoreuxia has a
 more restricted distribution in the Americas. Amoreuxia is comprised of
 four herbaceous species, and Cochlospermum has seven tree species and five
 that are suffrutescent subshrubs. The two genera also differ in floral
 symmetry, corolla coloration patterns, and stamen morphology. The goals of
 this study were to reconstruct the phylogeny of Cochlospermaceae to
 evaluate the monophyly of the family and its two genera, to resolve
 interspecific relationships, and to interpret patterns of morphological
 evolution. In addition, a minor goal was to examine its relationship to
 sister families, such as Bixaceae, a family in which Cochlospermaceae has
 been variously placed. Phylogenetic analyses were carried out using DNA
 sequences of the following markers: nuclear ribosomal ITS and the
 chloroplast trnG and trnL-F regions. The data support the monophyly of
 Cochlospermaceae and its distinctiveness from its sister families. While
 Amoreuxia is supported as monophyletic, Cochlospermum is paraphyletic with
 two species (C. orinocense and C. tetraporum) consistently placed outside
 a clade of all remaining Cochlospermum species. Ancestral character state
 reconstructions of morphology indicate that the tree habit may be
 ancestral in Cochlospermaceae with a single shift to an herbaceous growth
 form in Amoreuxia with the suffrutescent growth form having arisen twice
 within Cochlospermum, once in South America and once in Africa. There has
 been a single shift in floral morphology from radial symmetry, solid
 yellow petals, and uniform stamens to bilateral symmetry, two-toned
 petals, and dimorphic stamens in Amoreuxia. Anthers with one apical pore
 found in core Cochlospermum species may be a reduction from anthers with
 two pores, such as those found in Amoreuxia and in C. orinocense and C.
 tetraporum. Seed shape supports the sister relationships within
 Cochlospermaceae, particularly within Amoreuxia.
description: ITS
 SequencesAlignment file with ITS
 sequences (ITS1, 5.8S, ITS2)ITSNUclearFinal.megChloroplast trnG SequencesAlignment file for trnG sequencestrnG.megChloroplast trnL-F SequencesAlignment File for trnL-F SequencestrnLF.meg
DOI: 10.5061/dryad.v25c2
title: Data from: Population genetic structure of eelgrass (Zostera marina) on the Korean coast: current status and conservation implications for future management

description: Seagrasses provide numerous ecosystem services for coastal and estuarine
 environments, such as nursery functions, erosion protection, pollution
 filtration, and carbon sequestration. Zostera marina (common name
 "eelgrass") is one of the seagrass bed-forming species
 distributed widely in the northern hemisphere, including the Korean
 Peninsula. Recently, however, there has been a drastic decline in the
 population size of Z. marina worldwide, including Korea. We examined the
 current population genetic status of this species on the southern coast of
 Korea by estimating the levels of genetic diversity and genetic structure
 of 10 geographic populations using eight nuclear microsatellite markers.
 The level of genetic diversity was found to be significantly lower for
 populations on Jeju Island [mean allelic richness (AR) = 1.92, clonal
 diversity (R) = 0.51], which is located approximately 155 km off the
 southernmost region of the Korean Peninsula, than for those in the South
 Sea (mean AR = 2.69, R = 0.82), which is on the southern coast of the
 mainland. South Korean eelgrass populations were substantially genetically
 divergent from one another (FST = 0.061-0.573), suggesting that limited
 contemporary gene flow has been taking place among populations. We also
 found weak but detectable temporal variation in genetic structure within a
 site over 10 years. In additional depth comparisons, statistically
 significant genetic differentiation was observed between shallow (or
 middle) and deep zones in two of three sites tested. Depleted genetic
 diversity, small effective population sizes (Ne) and limited connectivity
 for populations on Jeju Island indicate that these populations may be
 vulnerable to local extinction under changing environmental conditions,
 especially given that Jeju Island is one of the fastest warming regions
 around the world. Overall, our work will inform conservation and
 restoration efforts, including transplantation for eelgrass populations at
 the southern tip of the Korean Peninsula, for this ecologically important
 species.
description: Raw dataset of eight
 microsatellite loci for the 16 populations_RametRaw dataset (ramets
 sampled) of eight microsatellite loci for the 16 populations from Jeju
 Island and the South Sea in KoreaRaw dataset of eight
 microsatellite loci for the 16 populations_GenetRaw dataset (genets) of
 eight microsatellite loci for the 16 populations from Jeju Island and the
 South Sea in Korea
DOI: 10.5061/dryad.s4k74
title: Data from: Differential influences of local subpopulations on regional diversity and differentiation for greater sage-grouse (Centrocercus urophasianus)

description: The distribution of spatial genetic variation across a region can shape
 evolutionary dynamics and impact population persistence. Local population
 dynamics and among-population dispersal rates are strong drivers of this
 spatial genetic variation, yet for many species we lack a clear
 understanding of how these population processes interact in space to shape
 within-species genetic variation. Here, we used extensive genetic and
 demographic data from 10 subpopulations of greater sage-grouse to
 parameterize a simulated approximate Bayesian computation (ABC) model and
 (i) test for regional differences in population density and dispersal
 rates for greater sage-grouse subpopulations in Wyoming, and (ii) quantify
 how these differences impact subpopulation regional influence on genetic
 variation. We found a close match between observed and simulated data
 under our parameterized model and strong variation in density and
 dispersal rates across Wyoming. Sensitivity analyses suggested that
 changes in dispersal (via landscape resistance) had a greater influence on
 regional differentiation, whereas changes in density had a greater
 influence on mean diversity across all subpopulations. Local
 subpopulations, however, varied in their regional influence on genetic
 variation. Decreases in the size and dispersal rates of central
 populations with low overall and net immigration (i.e. population sources)
 had the greatest negative impact on genetic variation. Overall, our
 results provide insight into the interactions among demography, dispersal
 and genetic variation and highlight the potential of ABC to disentangle
 the complexity of regional population dynamics and project the genetic
 impact of changing conditions.
description: Microsatellite genotypes
 for greater sage-grouse.Microsatellite genotypes
 (number of repeats for 14 loci) for 781 individuals from 10 subpopulations
 of the greater sage-grouse in Wyoming.rowetal_mol_ecol_2016.csv
DOI: 10.5061/dryad.kk61p
title: Data from: Indirect effects of global change accumulate to alter plant diversity but not ecosystem function in alpine tundra

description: 1. Environmental change can affect species directly by altering their
 physical environment and indirectly by altering the abundance of
 interacting species. A key challenge at the interface of community ecology
 and conservation biology is to predict how direct and indirect effects
 combine to influence response in a changing environment. In particular,
 little is known about how direct and indirect effects on biodiversity
 develop over time or their potential to influence ecosystem function. 2.
 We studied how nitrogen (N), winter precipitation (snow), and warming
 influenced diversity and ecosystem function over six years in alpine
 tundra. We used path analyses to partition direct effects of environmental
 manipulations from indirect effects due to changes in the abundance of two
 dominant plants. We hypothesize that 1) indirect effects will develop more
 slowly but will become stronger than direct effects over time, and 2)
 after six years, indirect effects will more strongly influence diversity
 while direct effects will influence ecosystem function. 3. Indirect
 effects of N on diversity were consistently stronger than direct effects
 and actually developed quickly, prior to direct effects. Direct effects of
 snow on diversity were detected in year two but then subsequently were
 reversed, while indirect effects were detected in year four and grew
 stronger over time. Overall in year six, indirect effects were much
 stronger than direct effects. 4. Direct effects predominated for three of
 four ecosystem functions we measured (productivity, N mineralization,
 winter N availability). The only indirect effects we found were that N and
 snow indirectly affected microbial biomass N by influencing Geum
 abundance. Across all four ecosystem measures, indirect effects were
 infrequent and weaker than direct effects. 5. Synthesis. Increasing
 indirect effects on diversity over time indicate that short-term
 experiments or monitoring of natural systems may underestimate the full
 magnitude of global change effects on plant communities. Explicitly
 accounting for changes in dominant plant abundance may be necessary for
 forecasting plant community response to environmental change. Conversely,
 weak indirect effects for ecosystem processes suggest that predicting
 ecosystem function without knowledge of plant responses to global change
 may be possible.
description: Plant community and
 ecosystem properties in a multifactor global change experiment on Niwot
 Ridge, Rocky Mountains COData are from a
 multifactor global change experiment, manipulating N, warming, and
 elevated snowpack in alpine tundra moist meadow. Data are from 2006-2012,
 although not every measurement was taken in all years; 2006 is
 pretreatment. Data collected are the following: species composition,
 productivity, litter mass, winter and summer N availability (resin),
 moisture, microbial biomass N and C, inorganic N, N mineralization,
 nitrification.Niwot_GlobalChangeExperiment_06to12Dryad.csv
DOI: 10.5061/dryad.kp18283
title: Data from: An optimized protocol for large-scale in situ sampling and analysis of volatile organic compounds

description: Chemical ecology is an ever‐expanding field with a growing interest in
 population‐ and community‐level studies. Many such studies are hindered
 due to lack of an efficient and accelerated protocol for large‐scale
 sampling and analysis of chemical compounds. Here, we present an optimized
 protocol for such large‐scale study of volatiles. A large‐scale in situ
 study to understand role of semiochemicals in variation in mating success
 of lekking blackbuck was conducted. Suitable methods for sampling and
 statistical analysis were identified by testing and comparing the
 efficiencies of available techniques to reduce analysis time while
 retaining sensitivity and comprehensiveness. Solid‐phase extraction using
 polydimethylsiloxane, analysis using a semiautomated detection of
 retention time and base peak, and statistical analysis using random forest
 algorithm were identified as the most efficient methods for large‐scale in
 situ sampling and analysis of volatiles. The protocol for large‐scale
 volatile analysis can facilitate evolutionary and metaecological studies
 of volatiles in situ from all types of biological samples. The protocol
 has potential for wider application with the analysis and interpretation
 methods being suitable for all kinds of semiochemicals, including
 nonvolatile chemicals.
description: Chemical
 DatasetLabelled chemical
 metadata file produced by the Perl code (GCMS Parser). Columns delineate
 sample ID, date of sampling, zone (P = peripheral, M = Middle, C =
 central), distance in meters from center, and the top 100 sampled volatile
 organic compounds (normalized relative ratios).BLACKBUCK
 DATA.csv