cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sk8rb66
title: Data from: Concurrent visual and motor selection during visual working memory guided action

description: Visual working memory enables us to hold onto past sensations in
 anticipation that these may become relevant for guiding future actions.
 Yet laboratory tasks have treated visual working memories in isolation
 from their prospective actions and have focused on the mechanisms of
 memory retention rather than utilization. To understand how visual
 memories become used for action, we linked individual memory items to
 particular actions and independently tracked the neural dynamics of visual
 and motor selection when memories became used for action. This revealed
 concurrent visual-motor selection, engaging appropriate visual and motor
 brain areas at the same time. Thus we show that items in visual working
 memory can invoke multiple, item-specific, action plans that can be
 accessed together with the visual representations that guide them,
 affording fast and precise memory-guided behavior.
description: s01s02s03s04s05s06s07s08s09s10s11s12s13s14s15s16s17s18s19s20s21s22s23s24s25README
DOI: 10.5061/dryad.85jn3
title: Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

description: Until recently, most phylogenetic and population genetics studies of
 nonhuman primates have relied on mitochondrial DNA and/or a small number
 of nuclear DNA markers, which can limit our understanding of primate
 evolutionary and population history. Here, we describe a cost-effective
 reduced representation method (ddRAD-seq) for identifying and genotyping
 large numbers of SNP loci for taxa from across the New World monkeys, a
 diverse radiation of primates that shared a common ancestor ~20-26 mya. We
 also estimate, for the first time, the phylogenetic relationships among 15
 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq
 SNP data using both maximum likelihood and quartet-based coalescent
 methods. Our phylogenetic analyses robustly reconstructed three
 monophyletic clades corresponding to the three families of extant
 platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as
 basal within the radiation. At the genus level, our results conformed well
 with previous phylogenetic studies and provide additional information
 relevant to the problematic position of the owl monkey (Aotus) within the
 family Cebidae, suggesting a need for further exploration of incomplete
 lineage sorting and other explanations for phylogenetic discordance,
 including introgression. Our study additionally provides one of the first
 applications of next-generation sequencing methods to the inference of
 phylogenetic history across an old, diverse radiation of mammals and
 highlights the broad promise and utility of ddRAD-seq data for molecular
 primatology.
description: Samples used in this
 studySamples used in the
 phylogenetic study. Each sample has an associated code that corresponds to
 the name of the files of the R1 and R2 raw reads.Samples_Study.xlsxData matrices of concatenated SNPs - iPYRADData matrices for the concatenated SNPs (.phy) for each one of the ipyrad assembly methods. .map files contains information about SNP position in each locus. This information will be used by tetrad to sample only one SNP per locus when analyzing each quartet sample in the analysis.DataMatrices_iPYRAD.tar.gzatelidae.tar.gzRaw reads for the samples belonging to the Atelidae familyOWM.tar.gzRaw reads for the samples belonging to the Old World Monkeyscebidae.tar.gzRaw reads for the samples belonging to the Cebidae familypitheciidae.tar.gzRaw reads for the samples belonging to the Pitheciidae family
DOI: 10.5061/dryad.tn39dc6
title: Data from: Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem

description: Despite decades of interest, few studies have provided evidence supporting
 theoretical expectations for coupled relationships between aboveground and
 belowground diversity and ecosystem functioning in non-manipulated
 naturalecosystems. We characterized plant species richness and density,
 soil bacterial, fungal and eukaryotic species richness and phylogenetic
 diversity (using 16S, ITS, and 18S gene sequencing), and ecosystem
 function (levels of soil C and N, and rates of microbial enzyme
 activities) along a natural gradient in plant richness and density in
 high-elevation, C-deficient soils to examine the coupling between above-
 and belowground systems. Overall, we observed a strong positive
 relationship between aboveground (plant richness and density) and
 belowground (bacteria, fungi, and non-fungal eukaryotes) richness. In
 addition to the correlations between plants and soil communities, C and N
 pools, and rates of enzyme activities increased as plant and soil
 communities became richer and more diverse. Our results suggest that the
 theoretically expected positive correlation between above- and belowground
 communities does exist in natural systems, but may be undetectable in late
 successional ecosystems due to the buildup of legacy organic matter that
 results in extremely complex belowground communities. In contrast,
 microbial communities in early successional systems, such as the system
 described here, are more directly dependent on contemporary inputs from
 plants and therefore are strongly correlated with plant diversity and
 density.
description: 16S_OTUTable16S OTUs generated through QIIME pipeline as described in the publication.16S_RepSetFasta file for representative 16S_OTUTable file16S_MapFileMapping file for QIIME pipeline along with metadata18S_OTUTable_NoFungi18S OTU Table generated with QIIME pipeline as described in the publication.18S_RepSetFasta file with representative sequences of OTUs in 18S_OTUTable file.18S_MapFileMapping file for QIIME pipeline along with metadataITS_OTUTableITS OTU Table generated with QIIME pipeline as described in the publicationITS_RepSetFasta file with representative sequences of the OTUs in ITS_OTUTable fileITS_MapFileMapping file for processing data in QIIME pipelineNematode_OTUTableNematode OTU table generated in QIIME as described in the publication.Nematode_RepSetFasta file for representative sequences within Nematode_OTUTable file.Nema_MapFileNematode mapping file for processing sequence data in QIIME along with metadata.NematodeSpecies_20gdswNematode species generated from Nematode_OTUTable file as described in the publication.NematodeSpecies_RepSetFasta file of representative sequences of nematode species in NematodeSpecies_OTUTable.Niwot 2015 Raw Sequence Data16S, 18S, and ITS raw sequence data along with indexing reads produced by Illumina MiSeq from field samples collected at Niwot Ridge, Colorado during 2015.Niwot_2015_SeqData.zip
DOI: 10.5061/dryad.dv920
title: Data from: Near-global freshwater-specific environmental variables for biodiversity analyses in 1km resolution

description: The lack of freshwater-specific environmental information at sufficiently
 fine spatial grain hampers broad-scale analyses in aquatic biology,
 biogeography, conservation, and ecology. Here we present a near-global,
 spatially continuous, and freshwater-specific set of environmental
 variables in a standardized 1 km grid. We delineate the sub-catchment for
 each grid cell along the HydroSHEDS river network and summarize the
 upstream climate, topography, land cover, surface geology and soil to each
 grid cell using various metrics (average, minimum, maximum, range, sum,
 inverse distance-weighted average and sum). All variables were
 subsequently averaged across single lakes and reservoirs of the Global
 lakes and Wetlands Database that are connected to the river network.
 Monthly climate variables were summarized into 19 long-term climatic
 variables following the ‘bioclim’ framework. This new set of variables
 provides a basis for spatial ecological and biodiversity analyses in
 freshwater ecosystems at near global extent, yet fine spatial grain. To
 facilitate the generation of freshwater variables for custom study areas
 and spatial grains, we provide the ‘r.stream.watersheds’ and
 ‘r.stream.variables’ add-ons for the GRASS GIS software.
description: ReadMeUpstream
 elevationelevation.ncUpstream flow accumulation and flow lengthflow_acc.ncUpstream surface geologygeology_weighted_sum.ncUpstream hydroclims (average & sum)hydroclim_average+sum.ncUpstream hydroclims (weighted average & weighted sum)hydroclim_weighted_average+sum.ncUpstream landcover (average)landcover_average.ncUpstream landcover (maximum)landcover_maximum.ncUpstream landcover (minimum)landcover_minimum.ncUpstream landcover (range)landcover_range.ncUpstream landcover (weighted average)landcover_weighted_average.ncMonthly upstream precipitation (sum)monthly_prec_sum.ncMonthly upstream precipitation (weighted sum)monthly_prec_weighted_sum.ncMonthly maximum upstream temperature (average)monthly_tmax_average.ncMonthly maximum upstream temperature (weighted average)monthly_tmax_weighted_average.ncMonthly minimum upstream temperature (average)monthly_tmin_average.ncMonthly minimum upstream temperature (weighted average)monthly_tmin_weighted_average.ncQuality control layersquality_control.ncUpstream slopeslope.ncUpstream soil (minimum)soil_minimum.ncUpstream soil (maximum)soil_maximum.ncUpstream soil (range)soil_range.ncUpstream soil (average)soil_average.ncUpstream soil (weighted average)soil_weighted_average.nc
DOI: 10.5061/dryad.k21r5
title: Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

description: Geographic variation in insect coloration is among the most intriguing
 examples of rapid phenotypic evolution and provides opportunities to study
 mechanisms of phenotypic change and diversification in closely related
 lineages. The bumble bee Bombus bifarius comprises two geographically
 disparate color groups characterized by red-banded and black-banded
 abdominal pigmentation, but with a range of spatially and phenotypically
 intermediate populations across western North America. Microsatellite
 analyses have revealed that B. bifarius in the USA are structured into two
 major groups concordant with geography and color pattern, but also suggest
 ongoing gene flow among regional populations. In this study, we better
 resolve the relationships among major color groups to better understand
 evolutionary mechanisms promoting and maintaining such polymorphism. We
 analyze &gt;90,000 and &gt;25,000 single-nucleotide polymorphisms
 derived from transcriptome (RNAseq) and double digest restriction site
 associated DNA sequencing (ddRAD), respectively, in representative samples
 from spatial and color pattern extremes in B. bifarius as well as
 phenotypic and geographic intermediates. Both ddRAD and RNAseq data
 illustrate substantial genome-wide differentiation of the red-banded
 (eastern) color form from both black-banded (western) and intermediate
 (central) phenotypes and negligible differentiation among the latter
 populations, with no obvious admixture among bees from the two major
 lineages. Results thus indicate much stronger background differentiation
 among B. bifarius lineages than expected, highlighting potential
 challenges for revealing loci underlying color polymorphism from
 population genetic data alone. These findings will have significance for
 resolving taxonomic confusion in this species and in future efforts to
 investigate color-pattern evolution in B. bifarius and other polymorphic
 bumble bee species.
description: Population Genomics Data
 for Bombus bifarius color pattern divergencedouble digest radseq and
 rnaseq files for samples across a color pattern and spatial transect for
 the widespread western North American bumble bee, Bombus bifarius. The
 included ZIP file contains raw sequence data as well as data files used
 for analysis.Lozier_Bbif_popgenomic_metadatadescriptor.txtFinal_Files_forDryad.zip
DOI: 10.5061/dryad.d36f5
title: Data from: Current geography masks dynamic history of gene flow during speciation in northern Australian birds

description: Genome divergence is greatly influenced by gene flow during early stages
 of speciation. As populations differentiate, geographical barriers can
 constrain gene flow and so affect the dynamics of divergence and
 speciation. Current geography, specifically disjunction and continuity of
 ranges, is often used to predict the historical gene flow during the
 divergence process. We test this prediction in eight meliphagoid bird
 species complexes codistributed in four regions. These regions are
 separated by known biogeographic barriers across northern Australia and
 Papua New Guinea. We find that bird populations currently separated by
 terrestrial habitat barriers within Australia and marine barriers between
 Australia and Papua New Guinea have a range of divergence levels and
 probability of gene flow not associated with current range connectivity.
 Instead, geographic distance and historical range connectivity better
 predict divergence and probability of gene flow. In this dynamic
 environmental context, we also find support for a nonlinear decrease of
 the probability of gene flow during the divergence process. The
 probability of gene flow initially decreases gradually after a certain
 level of divergence is reached. Its decrease then accelerates until the
 probability is close to zero. This implies that although geographic
 connectivity may have more of an effect early in speciation, other factors
 associated with higher divergence may play a more important role in
 influencing gene flow midway through and later in speciation. Current
 geographic connectivity may then mislead inferences regarding potential
 for gene flow during speciation under a complex and dynamic history of
 geographic and reproductive isolation.
description: ND2_alignmentsND2 alignments separated by different species or species complex.SDM_data.tarSpecies distribution modeling data including occurrence points, R output, and historical climate layers.Entomyzon_cyanotis_ddRADSorted bam files of ddRAD reads mapped onto a reference.Gerygone_magnirostris_ddRADSorted bam files of ddRAD reads mapped onto a reference.Lichmera_indistincta_ddRADSorted bam files of ddRAD reads mapped onto a reference.Melithreptus_albogularis_ddRADSorted bam files of ddRAD reads mapped onto a reference.Myzomela_obscura_ddRADSorted bam files of ddRAD reads mapped onto a reference.Philemon_buceroides_ddRADSorted bam files of ddRAD reads mapped onto a reference.Philemon_citreogularis_ddRADSorted bam files of ddRAD reads mapped onto a reference.Ptilotula_flavescens_fuscus_ddRADSorted bam files of ddRAD reads mapped onto a reference.
DOI: 10.5061/dryad.cs41886
title: Data from: Reproductive isolation in alpine gingers: how do co-existing Roscoea (R. purpurea and R. tumjensis) conserve species integrity?

description: Multiple barriers may contribute to reproductive isolation between closely
 related species. Understanding the relative strength of these barriers can
 illuminate the ecological factors that currently maintain species
 integrity and how these factors originally promoted speciation. Two
 Himalayan alpine gingers, Roscoea purpurea and R. tumjensis, occur
 sympatrically in central Nepal and have such similar morphology that it is
 not clear whether or how they maintain a distinct identity. Our
 quantitative measurements of the components of reproductive isolation show
 that they are, in fact, completely isolated by a combination of
 phenological displacement of flowering, earlier for R. tumjensis and later
 for R. purpurea, and complete fidelity of visitation by different
 pollinator species, bumblebees for R. tumjensis and a long-tongued fly for
 R. purpurea. Furthermore, the nectar of R. tumjensis flowers is available
 to the shorter-tongued bumblebees while R. purpurea nectar is less
 accessible, requiring deep probing from long-tongued flies. Although
 flowering phenology is a strong current barrier that seemingly obviates
 any need for pollinator discrimination, this current pattern need not
 reflect selective forces occurring at the initial divergence of R.
 tumjensis. There has been considerable pollinator switching during the
 radiation of the Himalayan Roscoea, and the association of flowering time
 with type of pollinator in these sympatric species may have originated
 among the earliest or latest flowering individuals or populations of an
 ancestor in order to exploit either bumblebee activity early in the
 breeding season or long-tongued fly abundance later in the season. These
 two sympatric Roscoea species add to accumulating evidence of the primacy
 of pre-zygotic pollination traits in speciation among angiosperms even in
 the absence of post-zygotic incompatibility.
description: Paudel et al
 2018_Reproductive isolation_evolution_DyradAll data collected
 through field experiment.
DOI: 10.5061/dryad.7851
title: Data from: Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)

description: The merger of two or more divergent genomes within an allopolyploid
 nucleus can facilitate speciation and adaptive evolution in flowering
 plants. Widespread changes to gene expression have been shown to result
 from interspecific hybridisation and polyploidy in a number of plant
 species, and attention has now shifted to determining the epigenetic
 processes which drive these changes. We present here an analysis of
 cytosine methylation patterns in triploid F1 Senecio (ragwort) hybrids and
 their allohexaploid derivatives. We observe that, in common with similar
 studies in Arabidopsis, Spartina and Triticum, a small but significant
 proportion of loci display nonadditive methylation in the hybrids, largely
 resulting from interspecific hybridisation. Despite this, genome
 duplication results in a secondary effect on methylation, with reversion
 to additivity at some loci and novel methylation status at others. We also
 observe differences in methylation state between different allopolyploid
 generations, predominantly in cases of additive methylation with regard to
 which parental methylation state is dominant. These changes to methylation
 state in both F1 triploids and their allohexaploid derivatives largely
 mirror the overall patterns of nonadditive gene expression observed in our
 previous microarray analyses and may play a causative role in generating
 those expression changes. These similar global changes to DNA methylation
 resulting from hybridisation and genome duplication may serve as a source
 of epigenetic variation in natural populations, facilitating adaptive
 evolution. Our observations that methylation state can also vary between
 different generations of polyploid hybrids suggests that newly-formed
 allopolyploid species may display a high degree of epigenetic diversity
 upon which natural selection can act.
description: Combined Genotypes
 TableExcel spreadsheet of
 binary allele calls for methylation-sensitive AFLP analysis of 33 Senecio
 plants. Primer combination (i.e. Eco+AAC/Mse+CTG) listed in each locus
 name.
DOI: 10.5061/dryad.rj592
title: Data from: How bees deter elephants: beehive trials with forest elephants (Loxodonta africana cyclotis) in Gabon

description: In Gabon, like elsewhere in Africa, crops are often sources of conflict
 between humans and wildlife. Wildlife damage to crops can drastically
 reduce income, amplifying poverty and creating a negative perception of
 wild animal conservation among rural people. In this context, crop-raiding
 animals like elephants quickly become “problem animals”. To deter
 elephants from raiding crops beehives have been successfully employed in
 East Africa; however, this method has not yet been tested in Central
 Africa. We experimentally examined whether the presence of Apis mellifera
 adansonii, the African honey bee species present in Central Africa, deters
 forest elephants (Loxodonta Africana cyclotis) from feeding on fruit
 trees. We show for the first time that the effectiveness of beehives as
 deterrents of elephants is related to bee activity. Empty hives and those
 housing colonies of low bee activity do not deter elephants all the time;
 but beehives with high bee activity do. Although elephant disturbance of
 hives does not impede honey production, there is a tradeoff between
 deterrence and the quantity of honey produced. To best achieve the dual
 goals of deterring elephants and producing honey colonies must maintain an
 optimum activity level of 40 to 60 bee movements per minute. Thus,
 beehives colonized by Apis mellifera adansonii bees can be effective
 elephant deterrents, but people must actively manage hives to maintain bee
 colonies at the optimum activity level.
description: Data on bees and
 elephants experiments in GabonThis file contains all
 data related to experiments on how bees deter elephants. Those data have
 been harvested in Gamba, Gabon, Central Africa.B.E.D.31.10.2015.csvData on bees activities and honey production correlationThis file contains data allowing correlation calculations between bees activities and honey production.B.E.D.31.10.2015.Cor.BAct.and.Honey.csvData on bees activities and variables correlationThis file contains data allowing calculations of correlations between bees activities and studied variablesB.E.D.31.10.2015.Cor.BAct.and.Var.csv
DOI: 10.5061/dryad.5cb5b
title: Data from: Effect of fuel deposition rate on departure fuel load of migratory songbirds during spring stopover along the northern coast of the Gulf of Mexico

description: Migrants are generally assumed to minimize their overall migration time by
 adjusting their departure fuel loads (DFL) in relation to anticipated and
 experienced fuel deposition rates (FDRs). We utilized a 21-yr long
 migration banding station dataset to examine the relationship between FDR
 and DFL during spring migration in six Nearctic-Neotropical migratory
 songbird species during stopover along the northern coast of the Gulf of
 Mexico (GOM) following trans-gulf flight. Estimates of fuel stores,
 stopover durations, and FDRs from our long term migration data set were
 combined to determine DFL. We expected and found that migrants across all
 six species adjust their DFL to the rate at which they deposit fuel
 reserves. This robust finding suggests that songbird migrants are
 sensitive to time constraints during spring passage presumably to
 fine-tune their stopover schedule in relation to experienced and
 anticipated habitat quality. Two of the species studied showed an effect
 of age on the FDR–DFL relationship: one was consistent with the
 expectation that older birds would be less sensitive to changes in FDR,
 while the second was contrary to our expectations and likely suggesting an
 age-dependent response to habitat quality. We found sex-dependent
 differences consistent with male DFL being more sensitive to FDR in only
 two of six species studied, and argue that both males and females are time
 constrained during spring passage in relation to arrival at breeding
 destinations. The positive relationship between FDR and DFL among all
 species and for age and sex groups in some species reflects a migration
 strategy sensitive to time.
description: DATA
 FILEDeparture fuel loads
 were regressed against fuel deposition rates. For each species, 3 separate
 regressions were performed: 1) All individuals, 2) only individuals of
 known sex regardless of age (sex was a factor), and 3) only individuals of
 the more specific age classes regardless of sex (age was a factor). All
 analyses, including the resampling process, were performed in R 3.1.2 (R
 Core Team 2015).