cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05qfttf32
title: Contrasting effects of tree origin and urbanization on invertebrate abundance and tree phenology

description: The ongoing wide-scale introduction of non-native plants across the world
 may negatively influence native invertebrate fauna, due to a lack of
 co-evolved traits related to the novel plants, e.g. unique phytochemicals
 or shifted phenology. Non-native plants, specifically trees, are common in
 urban environments, areas that already pose novel habitats to plants and
 wildlife through a wide array of anthropogenic factors. For example,
 impervious surfaces contribute to increased ambient temperatures, the
 so-called urban heat island effect (UHI), which can affect local plant
 phenology. Yet, few studies have simultaneously studied the effects of
 urbanization and tree species origin on urban invertebrate communities. We
 measured the city-level UHI and phenology of nine native and seven
 non-native tree species in five city-centre parks in Southern Sweden, as
 well as four common native species in a rural control forest. We
 quantified the abundance of invertebrates on a subset of native and
 non-native tree species through shake-sampling, sticky-traps and frass
 collection. In the urban environment, non-native trees hosted
 significantly fewer invertebrates compared to native trees. Furthermore,
 the non-native trees had a delayed phenology compared to native species,
 while the peak of caterpillars associated with the subset of trees
 surveyed for this measure was significantly earlier compared to that of
 the native species studied. The effect of tree species origin on urban
 invertebrate abundance was of a greater magnitude (effect size) than the
 effect of urbanization on invertebrate abundance in native tree hosts.
 Hence, the results indicate that the impact of non-native vegetation may
 be a stronger driver of invertebrate declines in urban areas than other
 factors. As the effect of species origin on tree phenology was at a level
 comparable to the urban effect, increasing prevalence of non-native
 vegetation can potentially obscure effects of urbanization on phenology in
 large-scale studies, as well as induce mis-matches to invertebrate
 populations. Since parks harbour a large proportion of urban biodiversity,
 native trees play a crucial role in such habitats and should not be
 considered replaceable by non-native species in terms of conservation
 value. --
DOI: 10.7280/d1wm43
title: One-to-one orthologs between Danaus plexippus and other insect species

description: Ortholog identification was performed between the gene models annotated in
 Danaus plexippus, Bombyx mori, and Drosophila melanogaster. The D.
 plexippus sequences are from an assembly obtained from an individual that
 belonged to a monarch population found in Irapuato, Mexico. 1-to-1
 orthologs were delineated as part of an analysis devised to determining
 the proportion of gene models with homology support in other Lepidoptera
 and D. melanogaster, and in relation to a previously published gene
 annotation of D. plexippus. Additionally, information from 1-to-1
 orthologs was used in the process of contig anchoring to the D. plexippus
 chromosomes and in the examination of the level of macro and microsynteny
 conservation in relation to B. mori and D. melanogaster.
description: One-to-one identification between the collection of
 protein-coding gene models that are part of the gene annotation OGS1_DpMex
 of <em>D. plexippus </em>and those in <em>B. mori
 </em>and <em>D. melanogaster </em>was done with
 OrthoFinder v2.2.6 under the settings –S diamond –M msa, using protein
 models retrieved either from NCBI or lepBase. The genomic coordinates of
 orthologs were established according to DpMex_v1 for <i>D. plexippus
 </i>(10.5281/zenodo.4470132) and GCF_000151625.1_ASM15162v1 for
 <i>B. mori</i>. As the assembly sequences of <i>B.
 mori</i> are not associated with particular chromosomes, we
 ultimately used a second-party chromosomal-based gene coordinates (http://sgp.dna.affrc.go.jp/ComprehensiveGeneSet/files/GenesetA.chromosome.gbrowse.gff.zip).
DOI: 10.5061/dryad.tmpg4f4zn
title: Phosphotyrosine peptide abundance in control and Cul5-deficient MCF10A cells

description: The Cullin 5 RING ligase complex inhibits Src activity and Src-dependent
 transformation of MCF10A epithelial cells, in part by targeting pY
 proteins such as pYCas for degradation by the ubiquitin-proteasome system
 (Teckchandani et al., 2014). Because overexpression of Cas alone did not
 phenocopy CRL5 inhibition (Teckchandani et al., 2014), we infer that CRL5
 down-regulates additional pY proteins that become limiting when Cas is
 over-expressed. We sought to identify such pY proteins by screening for pY
 peptides whose abundance increases when Cul5 is inhibited. To this end,
 control and Cul5-deficient MCF10A cells were lysed under denaturing
 conditions, proteins were digested with trypsin, and peptides were labeled
 with isobaric TMT tags for quantitative pY proteomics (Zhang et al.,
 2007). In one experiment, samples were prepared from control and
 Cul5-deficient cells that were starved for epidermal growth factor (EGF)
 for 0, 24 or 72 hr. Starvation time had no systematic effect on peptide
 abundance, so, in a second experiment, we prepared biological triplicate
 samples from growing control and Cul5-deficient cells. Sixteen pY peptides
 increased significantly in Cul5-deficient cells in both experiments,
 including pY128 from Cas and pY117 and pY266 from BCAR3.
description: Two independent experiments were performed.
 141231_85_CP_Cul5_6plex_pY_psms paired samples of MCF10A shCont
 and shCul5 shifted to assay media for 0, 24 hr or 72 hr
 160825_297_CP_10A_shCUL5     paired samples of MCF10A shCont and
 shCul5 in growth media, biological triplicates Each
 experiment used TMT 6-plex iTRAQ labeling.  
description: Two files are provided for each experiment. (a) The .raw files.
 (b) Excel spreadsheets showing calculations. Please
 note that 160825_297_CP_sup.raw is the .raw file for peptides that did not
 bind to the anti-phosphotyrosine column. Methods are
 described in the linked publication.
DOI: 10.5061/dryad.p2ngf1vqv
title: Mass spectrometry of natively decorated doublet microtubule from Tetrahymena thermophila WT and mutants

description: Cilia are thin microtubule-based protrusions of eukaryotic cells. The
 swimming of ciliated protists and sperm cells is propelled by the beating
 of cilia. Cilia propagate the flow of mucus in the trachea and protect the
 human body from viral infections. The main force generators of ciliary
 beating are the outer dynein arms (ODAs) which attach to the doublet
 microtubules. The bending of cilia is driven by the ODAs'
 conformational changes caused by ATP hydrolysis. Here, we report the
 native ODA complex structure attaching to the doublet microtubule by
 cryo-electron microscopy and mass spectrometry. The structure reveals how
 the ODA complex is attached to the doublet microtubule via the docking
 complex in its native state. Combined with coarse-grained molecular
 dynamics simulations, we present a model of how the attachment of the ODA
 to the doublet microtubule induces remodeling and activation of the ODA
 complex.
description: Cilia were purified from Tetrahymena thermophila wild types and
 mutants. The dataset contains both ATP-induced splitted doublet
 microtubule or salt-treated doublet microtubules.
DOI: 10.5061/dryad.37pvmcvkh
title: The effects of salinity and N:P on N-rich toxins by both an N-fixing and non-N-fixing cyanobacteria

description: Freshwater ecosystems are experiencing increased salinization. Adaptive
 management of harmful algal blooms (HABs) contribute to
 eutrophication/salinization interactions through the hydrologic transport
 of blooms to coastal environments. We examined how nutrients and salinity
 interact to affect growth, elemental composition, and cyanotoxin
 production/release in two common HAB genera. Microcystis aeruginosa
 (non-nitrogen (N)-fixer and microcystin-LR producer; MC-LR) and
 Aphanizomenon flos-aquae (N-fixer and cylindrospermopsin producer; CYN)
 were grown in N:phosphorus (N:P) 4 and 50 (by atom) for 21 and 33 days,
 respectively, then dosed with a salinity gradient (0 – 10.5 g L-1). Both
 total MC-LR and CYN were correlated with particulate N. We found
 Microcystis MC-LR production and release was affected by salinity only in
 the N:P 50 treatment. However, Aphanizomenon CYN production and release
 was affected by salinity regardless of N availability. Our results
 highlight how cyanotoxin production and release across the freshwater –
 marine continuum are controlled by eco-physiological differences between
 N-acquisition traits.
DOI: 10.5061/dryad.2fqz612pd
title: Data from: Partitioning resources through the seasons: abundance and phenology of carrion beetles (Silphidae) in southeastern Ontario

description: The coexistence of ecologically similar species is thought to require
 resource partitioning to minimize competition. Phenological, seasonal
 differences in activity may provide an important axis for resource
 partitioning. Here, we test for evidence of seasonal differences in
 activity within a diverse guild of carrion beetles (Silphidae) in a
 habitat preserve on the Frontenac Arch, southeastern Ontario, Canada using
 a large-scale survey during their active seasons (April to October). We
 then used generalized additive models to test for differences in seasonal
 abundance among eight co-occurring carrion beetle species, including five
 species of burying beetles (Nicrophorinae: Nicrophorus Fabricius, 1775)
 and three species from the Silphinae subfamily. Consistent with previous
 work, all species showed seasonal variation in abundance, with peak
 abundance of most species occurring between June and August. All but one
 species (Nicrophorus sayi Laporte, 1840) showed positive relationships
 between abundance and temperature. We find evidence consistent with
 seasonal partitioning of resources among Nicrophorus habitat generalists
 that could potentially reduce competition for limited carrion resources.
 In contrast, we find little evidence for seasonal differences in abundance
 among Nicrophorus habitat specialists, which instead may partition
 resources spatially. Overall, our results provide evidence consistent with
 an important role for seasonal resource partitioning among carrion beetle
 species that show higher levels of spatial (habitat) overlap within a
 temperate beetle guild.
description: Data are raw counts. See Methods for details of collection.
description: See README file for description of variables, R code for
 analysis, and Methods in the original paper for details.
DOI: 10.5061/dryad.bnzs7h4bh
title: Predation shapes behavioral lateralization: insights from an adaptive radiation of livebearing fish

description: Hemispheric brain lateralization can drive the expression of behavioral
 asymmetry, or laterality, which varies notably both within and among
 species. To explain these left–right behavioral asymmetries in animals,
 predator-mediated selection is often invoked. Recent studies have
 revealed that a relatively high degree of
 lateralization correlates positively with traits known to confer
 survival benefits against predators, including escape performance,
 multitasking abilities, and group coordination. Yet, we still know
 comparatively little about 1) how consistently predators shape behavioral
 lateralization, 2) the importance of sex-specific variation, and 3) the
 degree to which behavioral lateralization is heritable. Here, we take
 advantage of the model system of the radiation of Bahamas
 mosquitofish (Gambusia hubbsi) and measure behavioral
 lateralization in hundreds of wild fish originating from
 multiple blue holes that differ in natural predation pressure. Moreover,
 we estimated the heritability of this trait using laboratory-born fish
 from one focal population. We found that the degree of
 lateralization but not the particular direction of lateralization
 (left or right) differed significantly across high and low predation risk
 environments. Fish originating from high-predation environments were more
 strongly lateralized, especially females. We further confirmed a genetic
 basis to behavioral lateralization in this species, with significant
 additive genetic variation in the population examined. Our results reveal
 that predation risk represents one key ecological factor that has likely
 shaped the origin and maintenance of this widespread behavioral
 phenomenon, even potentially explaining some of the sex-specific patterns
 of laterality recently described in some animals. 
description: Data for this study comprises individual behavioural
 lateralization scores of Bahamas mosquitofish assayed in a detour
 test (two-way T-maze arena) and consist of: 1.
 Lateralization scores from wild-caught fish originating from six
 different blue holes on Andros Island, The Bahamas: three high-predation
 blue holes (Cousteau´s, Stalactite and West Twin) and three low-predation
 blue holes (East Twin, Hubcap and Rainbow).  2.
 Lateralization scores from second-generation laboratory-raised fish
 derived from one of the focal high-predation regimes blue holes
 (Cousteau's) to test for genetic variation (i.e.
 heritability).
DOI: 10.5061/dryad.rjdfn2zbp
title: Avian community mist net survey data from Luba/Ureca road elevational gradient, Bioko Island, Equatorial Guinea

description: Understanding interactive effects between anthropogenic
 disturbance and abiotic factors on species turnover can help identify and
 prioritize conservation of potentially vulnerable tropical bird
 communities. We investigated potential factors influencing
 avian understory community composition along a recently
 constructed road across three elevations (300, 800 and 1200
 m), each with two sampling sites (road edge vs interior
 forest), over a four-year period on Bioko
 Island, Equatorial Guinea. Obligate ant following species were
 the most abundant guild sampled accounting for
 23% of total species diversity within the data set,
 which increased to 40% when including occasional ant following
 species. Habitat associated with elevation was
 the most significant factor influencing the composition of avian
 communities at all three elevations.
  Additionally, we identified species with clear statistical associations for each elevation: the yellow-lored bristlebill (Bleda notatus), olive sunbird (Cyanomitra obscura), and white-tailed warbler (Poliolias lopezi). We found evidence for significant community differences between the disturbance edge and interior forest transects at 300 m only. Likewise, understory insectivores were found at higher numbers within the interior forest transect at this elevation. Based on the data presented here, we suggest low elevation avian understory insectivores should be considered focal species for future assessment studies in this area. Furthermore, since many traditional protected areas focus on upland habitat containing high species endemism, our findings emphasize the importance of equally conserving lowland elevations as they may house commonly overlooked yet important and diverse segments of the bird community. 
description: Data was collected via mist net capture and processed using mixed
 modeling with the package "lme4" and ordination using non-metric
 multidimensional scaling with the package "vegan" in
 R.
description: Readme file uploaded
DOI: 10.5281/zenodo.18396458
title: Data for Measurement report: Role of synoptic circulation in regional ozone pollution over the Twain-Hu region of China: Dynamic source contribution and modulation mechanism
DOI: 10.5281/zenodo.18396459
title: Data for Measurement report: Role of synoptic circulation in regional ozone pollution over the Twain-Hu region of China: Dynamic source contribution and modulation mechanism
DOI: 10.5061/dryad.wh70rxwnn
title: Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds

description: The role of historical factors in establishing patterns of diversity in
 tropical mountains has been of interest for some time. In these regions,
 the historical processes of range fragmentation and contraction followed
 by dispersal are thought to be mediated by the interplay between rugged
 relief and climate fluctuations and likely explain most of the dynamics of
 diversification in plants and animals. Although empirical studies
 addressing the interaction between climate and topography have provided
 invaluable insights into population divergence and speciation patterns in
 tropical montane organisms, a more detailed and robust test of such
 processes in an explicit spatio-temporal framework is still lacking.
 Consequently, our ability to gain insights into historical range shifts
 over time and the genomic footprint left by them is limited. Here we used
 niche modeling and subgenomic population-level datasets to explore the
 evolution of two species of warbling finches disjunctly distributed across
 the Montane Atlantic Forest, a Neotropical
 region with complex geological and environmental
 histories. Population structure inferences suggest a scenario of three
 genetically differentiated populations, which are congruent with both
 geography and phenotypic variation. Demographic simulations support
 asynchronous isolation of these populations as recently as ~40
 kya, relatively stable population sizes over recent time, and past gene
 flow subsequent to divergence. Throughout the last 800 ky, niche models
 predicted extensive expansion into lowland areas with increasing overlap
 of species distributions during glacial periods, with prominent
 retractions and isolation into higher altitudes during interglacials,
 which are in line with signs of introgression of currently isolated
 populations. These results support a dual role of cyclical climatic
 changes: population divergence and persistence in mountain tops during
 warm periods followed by periods of expansion and admixture in lower
 elevations during cold periods. Shallow genetic divergence could be
 associated with undiscovered cryptic diversity in this global biodiversity
 hotspot.
DOI: 10.5061/dryad.m0cfxpp44
title: Do cogovernance and CSOs supplement municipal capacity for service delivery? An assessment of differences in simple versus complex services

description: Municipal governments in the Global South vary in their ability to provide
 not only complex social services, like environmentally proper solid waste
 disposal, but even simple services, like trash collection from the
 streets. This paper examines whether variation in service provision
 outcomes is associated with service-specific municipal administrative
 capacity, locally embedded civil society organization (CSO) presence, and
 collaborative governance for local planning and budgeting (or
 cogovernance). Using a panel dataset of Peruvian municipalities, I find
 that while all three factors are associated with better outcomes for
 simple services, only greater public administration capacity is associated
 with higher service outcomes when the service is more complex. This
 suggests that CSOs may face some difficulties to supplement the state in
 the provision of relatively complex services and that local cogovernance
 venues tend to prioritize more immediate service issues. These findings
 have policy implications for managing relatively complex services
 in Global South cities that struggle with service-specific
 administrative capacity and relatively complex service provision,
 particularly those with climate change consequences. They convey
 that strengthening this type of capacity at the office level is crucial to
 providing increasingly complex services, and engaging community-based CSOs
 and cogovernance venues may help as a strategy to address simple service
 delivery.
DOI: 10.5061/dryad.j3tx95xds
title: Insect-mediated apparent competition between mammals in a boreal food web

description: Datasets generated and analyzed within the study area located in
 the Côte-Nord region of Québec, Canada.
 "DataFinal_Vegetation.csv" was used to evaluate the
 availability of deciduous vegetation (column Cover_Deciduous) in stands
 impacted by the spruce budworm (SBW, severity index values presented in
 column SBW_SevCum) outbreak and test our prediction that the reduction in
 canopy cover caused by SBW in coniferous stands would result in greater
 deciduous vegetation. We determined the percentage cover of deciduous
 vegetation for two height strata ([0-1m] and [1-3m] classes,
 column Stratum). "DataFinal_Moose_density.csv" was used
 to assess the influence of SBW outbreak (SBW_SevCum) on moose
 abundance by comparing moose densities (Density) before (year =
 2006) and during SBW outbreak (year = 2018). We also determined the effect
 of the percentage cover of deciduous vegetation (Broadleaf)
 and the percentage cover of salvage-logged forest stands
 (SBW_cut_2018Factor) on moose densities.
 "DataFinal_RSF_Caribou.csv" and
 "DataFinal_RSF_Wolves.csv" were used to
 develop Resource Selection Functions for caribou and wolves to
 assess habitat selection. RSFs compare resource characteristics of
 observed (scored 1) and random (scored 0) locations presented in column
 case. Habitat characteristics (columns conif_dense, conif_open,
 mixed, open, other, burned0_5, burned6_20, burned21_, cut0_5, cut6_20,
 cut21_) was extracted from the Canadian National Forest Inventory
 (NFI) forest cover maps. Land cover maps were updated every year by adding
 roads, recent (&lt;5 years), regenerating (6–20 years) and old (21–50
 years) cutblocks/fires based on information provided annually by local
 forestry companies and from the Canadian National Fire Database (CNFDB).
 SBW outbreak was characterized by its cumulative severity
 (SBW_SevCum), and also if infested stands were logged (SBW_Cut). As our
 study focused on the survival of boreal caribou, we added the mortality
 status for each individual  (DeadStatus, remained alive
 throughout the study = 0, died = 1) and interaction
 terms (i.e. the multiplication of two columns) Dead_SBW_SevCum
 and Dead_SBW_Cut.  Finally, we used
 "DataFinal_SurvivalAnalysis.csv" to evaluate whether
 the proportion of natural (Prop_burned) and anthropogenic (Prop_Cut0_5,
 Prop_Cut6_20, Prop_SBW_cut) disturbances within winter home range
 had an effect on the mortality risk of caribou (determined with the
 mortality status column Dead : remained alive throughout the
 study = 0, died = 1). For this analysis, we determined the
 individual ID (ID), the years during they were monitored (Year), and the
 time was defined as the total period of monitoring for that
 individual (Time). 
description: All the methods are detailed in the article: Labadie G. et
 al. Insect-mediated apparent competition between mammals in a boreal food
 web, Papers "in press" at PNAS.