cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4088k
title: Data from: Active farmsteads are year-round strongholds for farmland birds

description: 1. Farmland birds have experienced substantial declines over recent
 decades and various conservation measures have been designed to halt their
 massive decrease. The effectiveness of these measures is however limited,
 due to inappropriate identification of crucial breeding and wintering
 habitats. Identification of appropriate habitats, like farmsteads, and
 understanding seasonal changes in species richness and abundance of
 farmland birds within these habitats may therefore be key for farmland
 bird conservation. 2. We investigated the effect of variation in farmstead
 management on alpha and gamma diversity of all farmland birds and
 red-listed farmland birds in the Czech Republic. In particular, we
 evaluated the diversity of wintering and breeding birds at over 200 sites
 to explore: i) differences in bird communities in three types of
 farmsteads and open farmland; ii) changes in species-specific habitat
 preferences between winter and spring; iii) effect of landscape
 composition, ruderal vegetation and altitude on bird assemblages. 3.
 Farmsteads with animal production harboured the highest, whereas open
 farmland areas had the lowest, species richness and abundance of all
 farmland birds and red-listed farmland birds. The decline of species
 richness in winter was more pronounced in farmland and abandoned
 farmsteads compared to farmsteads with plant and animal production. 4.
 Single bird species showed different habitat preferences but the majority
 of species including red-listed farmland birds changed preferences toward
 animal farmsteads during winter. Bird species richness was negatively
 correlated with altitude and positively with representation of ruderal
 vegetation. Rarefied gamma diversity confirmed local patterns for both all
 species and red-listed species: the highest total species richness was
 observed in active animal farmsteads but differences among types were
 significant only during winter. 5. Synthesis and applications. Active
 farmsteads are local bird diversity hotspots in an agricultural landscape
 and host species of conservation concern. Our results highlighted the
 importance of farmsteads during winter, which is a critical period for
 several wintering farmland species. Our research thus indicates that
 recent conservation measures for farmland birds should also focus on
 conservation within non-farmed habitats, such as actively used farmsteads.
description: List of farmland bird
 species recorded in four habitat typesList of farmland bird
 species recorded in four habitat types (animal farmsteads, plant
 farmsteads, abandoned farmsteads and farmland). Sum of maximal numbers of
 recorded individuals during spring and winter period are shown. Red-listed
 birds are marked with red colour.Appendix_S1.docxCCA showing distribution of bird species among studied habitat typesCanonical correspondence analysis plots showing distribution of bird species among studied habitat types in spring (left plot) and winter (right plot). Red-listed birds are marked with red colour.Appendix S2.docx
DOI: 10.5061/dryad.t1715
title: Data from: Latitudinal patterns of herbivore pressure in a temperate herb support the biotic interactions hypothesis

description: The longstanding biotic interactions hypothesis predicts that herbivore
 pressure declines with latitude, but the evidence is mixed. To address
 gaps in previous studies, we measured herbivory and defense in the same
 system, quantified defense with bioassays, and considered effects of leaf
 age. We quantified herbivory and defense of young and mature leaves along
 a continental gradient in eastern North America in the native herb
 Phytolacca americana. Herbivory in the field declined with latitude and
 was strongly correlated with Lepidopteran abundance. Laboratory bioassays
 revealed that leaf palatability was positively correlated with latitude of
 origin. Young leaves were more damaged than mature leaves at lower
 latitudes in the field, but less palatable in bioassays. Both defense and
 palatability displayed non-linear latitudinal patterns, suggesting
 potential mechanisms based on biological or climatic thresholds. In sum,
 observational and experimental studies find patterns consistent with high
 herbivore pressure and stronger plant defenses at lower latitudes.
description: Herbivory on Phytolacca
 americana from Michigan to Florida in fieldbaskett_herbiv_lat_PHAM.csvLepidopteran herbivores collected from Phytolacca americana from Michigan to Floridabaskett_leps_lat_PHAM.csvPalatability of Phytolacca americana from Michigan to Florida in labbaskett_palatability_lat_PHAM.csv
DOI: 10.5061/dryad.5ms6g
title: Data from: Population signatures of large-scale, long-term disjunction and small-scale, short-term habitat fragmentation in an Afromontane forest bird

description: The Eastern Afromontane cloud forests occur as geographically distinct
 mountain exclaves. The conditions of these forests range from large to
 small and from fairly intact to strongly degraded. For this study, we
 sampled individuals of the forest bird species, the Montane White-eye
 Zosterops poliogaster from 16 sites and four mountain archipelagos. We
 analysed 12 polymorphic microsatellites and three phenotypic traits, and
 calculated Species Distribution Models (SDMs) to project past
 distributions and predict potential future range shifts under a scenario
 of climate warming. We found well-supported genetic and morphologic
 clusters corresponding to the mountain ranges where populations were
 sampled, with 43% of all alleles being restricted to single mountains. Our
 data suggest that large-scale and long-term geographic isolation on
 mountain islands caused genetically and morphologically distinct
 population clusters in Z. poliogaster. However, major genetic and
 biometric splits were not correlated to the geographic distances among
 populations. This heterogeneous pattern can be explained by past climatic
 shifts, as highlighted by our SDM projections. Anthropogenically
 fragmented populations showed lower genetic diversity and a lower mean
 body mass, possibly in response to suboptimal habitat conditions. On the
 basis of these findings and the results from our SDM analysis we predict
 further loss of genotypic and phenotypic uniqueness in the wake of climate
 change, due to the contraction of the species’ climatic niche and
 subsequent decline in population size.
description: Appendix
 S1_Dryad_Heredity_Habel et al.Allele frequencies of
 microsatellites
DOI: 10.5061/dryad.0h4v8
title: Data from: Direct effects of microalgae and protists on herring (Clupea harengus) yolk sac larvae

description: This study investigated effects of microalgae (Rhodomonas baltica) and
 heterotrophic protists (Oxyrrhis marina) on the daily growth, activity,
 condition and feeding success of Atlantic herring (Clupea harengus) larvae
 from hatch, through the end of the endogenous (yolk sac) period. Yolk sac
 larvae were reared in the presence and absence of microplankton and, each
 day, groups of larvae were provided access to copepods. Larvae reared with
 microalgae and protists exhibited precocious (2 days earlier) and ≥ 60%
 increased feeding incidence on copepods compared to larvae reared in only
 seawater (SW). In the absence and presence of microalgae and protists,
 survival and growth trajectories of yolk sac larvae were similar and
 digestive enzyme activity (trypsin) and nutritional condition (RNA-DNA
 ratio) markedly declined in all larvae directly after yolk sac depletion.
 Thus, microplankton promoted early feeding but was not sufficient to alter
 survival and growth during the yolk sac phase. Given the importance of
 early feeding, field programs should place greater emphasis on the
 protozooplankton-ichthyoplankton link to better understand match-mismatch
 dynamics and bottom-up drivers of year class success in marine fish.
description: S1_datasetThis study investigated effects of microalgae (Rhodomonas baltica) and heterotrophic protists (Oxyrrhis marina) on the daily growth, activity, condition and feeding success of Atlantic herring (Clupea harengus) larvae from hatch, through the end of the endogenous (yolk sac) period. Yolk sac larvae were reared in the presence and absence of microplankton and, each day, groups of larvae were provided access to copepods. Larvae reared with microalgae and protists exhibited precocious (2 days earlier) and ≥ 60% increased feeding incidence on copepods compared to larvae reared in only seawater (SW). In the absence and presence of microalgae and protists, survival and growth trajectories of yolk sac larvae were similar and digestive enzyme activity (trypsin) and nutritional condition (RNA-DNA ratio) markedly declined in all larvae directly after yolk sac depletion. Thus, microplankton promoted early feeding but was not sufficient to alter survival and growth during the yolk sac phase. Given the importance of early feeding, field programs should place greater emphasis on the protozooplankton-ichthyoplankton link to better understand match-mismatch dynamics and bottom-up drivers of year class success in marine fish.
DOI: 10.5061/dryad.td1g2
title: Data from: Plasticity in social communication and its implications for the colonization of novel habitats

description: Behavioral plasticity is expected to facilitate the colonization of novel
 habitats by allowing populations to respond rapidly to abrupt
 environmental change. We studied contextual plasticity—a form of
 plasticity that allows an immediate phenotypic response to stimuli—in the
 territorial communication of Puerto Rican Anolis lizards and considered
 the role it might play in facilitating colonization. In these lizards, the
 detection of territorial visual displays by receivers is acutely dependent
 on fluctuating levels of visual noise from windblown vegetation and
 ambient light. We quantified the contextual reaction norms of various
 components of the territorial displays of individual lizards as a function
 of visual noise and light for one focal population over many weeks of
 observation. We then compared these contextual reaction norms to the
 displays given by closely related Anolis species found in other
 environments to assess the extent to which colonizing lizards might be
 capable of performing displays similar to those likely to be effective in
 those environments. Our results suggest that lizards are able to rapidly
 adjust their territorial displays in ways that might help them communicate
 in other (but not all) habitat types on Puerto Rico. Given that the
 contextual plasticity of animal signals can be measured in free-living
 animals far more easily than other forms of behavioral plasticity, our
 study presents animal communication as a tractable model for tackling
 broad questions in how phenotypic plasticity might facilitate
 colonization, adjustment to environmental change, and adaptation.
description: Ord_TJ-BEHECO-2015-0352R2_HBspeedData on the maximum speed of headbob movements for 14 adult male Anolis gundlachiOrd_TJ-BEHECO-2015-0352R2_HBdurationData on the duration of headbob display bouts for 14 adult male Anolis gundlachiOrd_TJ-BEHECO-2015-0352R2_PSynchData on PSynch (relation of headbob bouts to dewlap extensions) for 14 adult male Anolis gundlachiOrd_TJ-BEHECO-2015-0352R2_PlasticityPredictorsData on the absolute plasticity estimated for the duration of headbob display bouts in response to fluctuations in habitat light for 14 adult male Anolis gundlachi
DOI: 10.5061/dryad.s6c68
title: Data from: Testing genotypic variation of an invasive plant species in response to soil disturbance and herbivory

description: Herbivores, competitors, and predators can inhibit biological invasions
 (“biotic resistance” sensu Elton 1959), while disturbance typically
 promotes biological invasions. Although biotic resistance and disturbance
 are often considered separately in the invasion literature, these two
 forces may be linked. One mechanism by which disturbance may facilitate
 biological invasions is by decreasing the effectiveness of biotic
 resistance. The effects of both disturbance and biotic resistance may vary
 across invading genotypes, and genetic variation in the invasive propagule
 pool may increase the likelihood that some genotypes can overcome biotic
 resistance or take greater advantage of disturbance. We conducted an
 experimental field trial in which we manipulated soil disturbance (thatch
 removal and loosening soil) and the presence of insect herbivores and
 examined their effects on the invasion success of 44 Medicago polymorpha
 genotypes. As expected, insecticide reduced leaf damage and increased
 Medicago fecundity, suggesting that insect herbivores in this system
 provide some biotic resistance. Soil disturbance increased Medicago
 fecundity, but did not alter the effectiveness of biotic resistance by
 insect herbivores. We found significant genetic variation in Medicago in
 response to disturbance, but not in response to insect herbivores. These
 results suggest that the ability of Medicago to invade particular habitats
 depends on the amount of insect herbivory, the history of disturbance in
 the habitat, and how the specific genotypes in the invader pool respond to
 these factors.
description: Medicago traits and
 fitnessPrimary data file
 containing data on Medicago height, flowering date, herbivore damage, and
 fruit number.for
 Dryad.xlsx
DOI: 10.5061/dryad.3rk33
title: Data from: Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus

description: Background: SBP-box genes belong to one of the largest families of
 transcription factors. Though members of this family have been
 characterized to be important regulators of diverse biological processes,
 information of SBP-box genes in the third most important oilseed crop
 Brassica napus is largely undefined. Results: In the present study, by
 whole genome bioinformatics analysis and transcriptional profiling, 58
 putative members of SBP-box gene family in oilseed rape (Brassica napus
 L.) were identified and their expression pattern in different tissues as
 well as possible interaction with miRNAs were analyzed. In addition, B.
 napus lines with contrasting branch angle were used for investigating the
 involvement of SBP-box genes in plant architecture regulation. Detailed
 gene information, including genomic organization, structural feature,
 conserved domain and phylogenetic relationship of the genes were
 systematically characterized. By phylogenetic analysis, BnaSBP proteins
 were classified into eight distinct groups representing the clear
 orthologous relationships to their family members in Arabidopsis and rice.
 Expression analysis in twelve tissues including vegetative and
 reproductive organs showed different expression patterns among the SBP-box
 genes and a number of the genes exhibit tissue specific expression,
 indicating their diverse functions involved in the developmental process.
 Forty-four SBP-box genes were ascertained to contain the putative miR156
 binding site, with 30 and 14 of the genes targeted by miR156 at the coding
 and 3′UTR region, respectively. Relative expression level of miR156 is
 varied across tissues. Different expression pattern of some BnaSBP genes
 and the negative correlation of transcription levels between miR156 and
 its target BnaSBP gene were observed in lines with different branch angle.
 Conclusions: Taken together, this study represents the first systematic
 analysis of the SBP-box gene family in Brassica napus. The data presented
 here provides base foundation for understanding the crucial roles of
 BnaSBP genes in plant development and other biological processes.
description: SBP-box genes in
 Brassica napus genomeSBP-box protein Brassica
 napus, rice and ArabidopsisSBP-box proteins in
 Brassica napus, rice and Arabidopsis
DOI: 10.5061/dryad.2dq7pf3
title: Data from: Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover (Trifolium repens)

description: Urbanization is a global phenomenon with profound effects on the ecology
 and evolution of organisms. We examined the relative roles of natural
 selection, genetic drift and gene flow in influencing the evolution of
 white clover (Trifolium repens), which thrives in urban and rural areas.
 Trifolium repens exhibits a Mendelian polymorphism for the production of
 hydrogen cyanide (HCN), a potent antiherbivore defence. We quantified the
 relative frequency of HCN in 490 populations sampled along urban-rural
 transects in 20 cities. We also characterized genetic variation within 120
 populations in eight cities using 16 microsatellite loci. HCN frequency
 increased by 0.6% for every km from an urban centre, and the strength of
 this relationship did not significantly vary between cities. Populations
 did not exhibit changes in genetic diversity with increasing urbanization,
 indicating that genetic drift is unlikely to explain urban-rural clines in
 HCN frequency. Populations frequently exhibited isolation-by-distance and
 extensive gene flow along most urban-rural transects, with the exception
 of a single city that exhibited genetic differentiation between urban and
 rural populations. Our results show that urbanization repeatedly drives
 parallel evolution of an ecologically important trait across many cities
 that vary in size, and this evolution is best explained by urban-rural
 gradients in natural selection.
description: Frequency of
 cyanogenesis within populations across 20 cities20_cities_cyano_poplevel.csvcity_meanvals_2017.12.24Mean values per city used in analyses. Intercept and slope refer to OLS regressions of cyanogenesis VS standardized distance8citiesSummary_gen div_2017.12.23Gene diversity statistics used in population genetic analyses. R file is "R_8citiesSummary_gen div_2017.12.24"R_8citiesSummary_gen div_2017.12.24R file used for genetic diversity analyses based on microsatts8cities16loci_pop_id_separatorsAllele calls at 16 microwatt loci for each individual used in DAPC analyses. Note the labels for the rows is in the file pops_genind_2018.1.27pops_genind_2018.1.27Individual levels labels formatted for hierarchical subsetting of dataDAPC_2018.1.27R script for DAPC analyses. Two files are used; older files included in the scripts are not included.R script for redundancy analysesThese scripts were used to test for isolation by distance and the effect of urbanization on genetic differentiation while controlling for IBD. There are a lot of individual files that go into these analyses. Available upon request to Marc Johnson (Marc.johnson@utoronto.ca).RDA.RR_20_cities_cyano_poplevel2017.12.23R file of all analyses done on population level stats of cyanogenesis. The R file also contains scripts performed on city_meanvals data (city mean values)
DOI: 10.5061/dryad.894jc22
title: Data from: Declining demographic performance and dispersal limitation influence the geographic distribution of the perennial forb, Astragalus utahensis (fabaceae)

description: 1. A central goal of ecology is understanding the determinants of species’
 distributions. ‘Metapopulation’ models for the existence of distributional
 boundaries predict that species’ geographic ranges arise from the
 landscape-scale deterioration of habitat suitability towards the range
 edge (i.e. niche mechanisms), which simultaneously hinders demographic
 performance and limits dispersal to suitable habitat beyond the edge (i.e.
 dispersal limitation). However, few studies have examined both of these
 mechanisms for the same species by examining abundance and comprehensive
 measures of demographic performance across the distribution and beyond its
 boundary. 2. We tested the predictions of metapopulation models for range
 limits by contrasting abundance, demographic performance, and population
 growth (λ) of the perennial forb Astragalus utahensis in central and
 northern range edge populations. We tested for dispersal limitation by
 transplanting individuals at and beyond the northern range boundary and
 monitoring their demographic performance. 3. Astragalus abundance and
 stochastic λ decreased from the range center to the northern range edge,
 with stochastic λ falling to or below replacement in range edge
 populations. However, transplants at some sites beyond the northern range
 edge survived and reproduced at levels similar to transplants within the
 range. Thus, in addition to deteriorating conditions at the range edge,
 dispersal limitation appears to contribute to limiting A. utahensis’
 northern distribution. 4. Synthesis: Our results support metapopulation
 models for range limits by suggesting that decreased demographic
 performance constrains the viability of range edge populations while
 contributing to dispersal limitation of A. utahensis’ distribution. Thus,
 the tandem action of niche and dispersal processes appears to play an
 important role in constraining this species’ northern latitudinal range.
description: Baer_&_Maron_JEcol_Data_&_CodeData and R Code associated with Baer & Maron, "Declining demographic performance and dispersal limitation influence the geographic distribution of the perennial forb, Astragalus utahensis (Fabaceae)" (Journal of Ecology)
DOI: 10.5061/dryad.75dg8
title: Data from: The case of the missing ancient fungal polyploids

description: Polyploidy—the increase in the number of whole chromosome sets—is an
 important evolutionary force in eukaryotes. Polyploidy is well recognized
 throughout the evolutionary history of plants and animals, where several
 ancient events have been hypothesized to be drivers of major evolutionary
 radiations. However, fungi provide a striking contrast: while numerous
 recent polyploids have been documented, ancient fungal polyploidy is
 virtually unknown. We present a survey of known fungal polyploids that
 confirms the absence of ancient fungal polyploidy events. Three hypotheses
 may explain this finding. First, ancient fungal polyploids are indeed
 rare, with unique aspects of fungal biology providing similar benefits
 without genome duplication. Second, fungal polyploids are not successful
 in the long term, leading to few extant species derived from ancient
 polyploidy events. Third, ancient fungal polyploids are difficult to
 detect, causing the real contribution of polyploidy to fungal evolution to
 be underappreciated. We consider each of these hypotheses in turn and
 propose that failure to detect ancient events is the most likely reason
 for the lack of observed ancient fungal polyploids. We examine whether
 existing data can provide evidence for previously unrecognized ancient
 fungal polyploidy events but discover that current resources are too
 limited. We contend that establishing whether unrecognized ancient fungal
 polyploidy events exist is important to ascertain whether polyploidy has
 played a key role in the evolution of the extensive complexity and
 diversity observed in fungi today and, thus, whether polyploidy is a
 driver of evolutionary diversifications across eukaryotes. Therefore, we
 conclude by suggesting ways to test the hypothesis that there are
 unrecognized polyploidy events in the deep evolutionary history of the
 fungi.
description: Alignment of genes from
 twenty-five fungiAlignment of genes used
 to generate phylogenetic tree of twenty-five fungal taxa for modelling
 genome and chromosome evolution.fungalAlignment.phyPartitioning scheme for alignment fileA RAxML formatted partition file for the sequence alignment file.fungalAlignmentPartition.txtGenome size and inferred ancestral states from MesquiteObserved genome sizes and inferred ancestral states in a nexus file for use with Mesquite from twenty-five fungi.MLTree.newickChromosome counts from fungiChromosome counts for the twenty-five fungi from the sequence alignment, for use with ChromEvol software.counts.txt