cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5ks03
title: Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex

description: Closely related species with divergent life-history traits are excellent
 models to infer the role of such traits in genetic diversity and
 connectivity. Ophioderma longicauda is a brittle star species complex
 composed of different genetic clusters, including brooders and
 broadcasters. These species diverged very recently and some of them are
 sympatric and ecologically syntopic, making them particularly suitable to
 study the consequences of their trait differences. At the scale of the
 geographic distribution of the broadcasters (Mediterranean Sea and
 north-eastern Atlantic), we sequenced the mitochondrial marker COI and
 genotyped an intron (i51) for 788 individuals. In addition, we sequenced
 10 nuclear loci newly developed from transcriptome sequences, for six
 sympatric populations of brooders and broadcasters from Greece. At the
 large scale we found a high genetic structure within the brooders (COI:
 0.07
description: fasta alignments: 11
 genetic markersThis folder contains the
 fasta alignments of the 11 genetic markers used in this study, for the
 Ophioderma longicauda clusters C3, C5 and C6. The sequences were obtained
 using Miseq sequencing.alignments_11_markers.zipraw_miseq_data_1this folder contains the raw Miseq data for the wells A1 to B10 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplifiedraw_miseq_data_2this folder contains the raw Miseq data for the wells B11 to D9 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplifiedraw_miseq_data_3this folder contains the raw Miseq data for the wells D10 to F11 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplifiedraw_miseq_data_4this folder contains the raw Miseq data for the wells F12 to H12 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplifiedsample sheet - individuals and position on the platethis excel file shows the pooling of PCR amplicons (38 markers used) for 288 individuals in a 96-well plate. In each well, the amplicons of three individuals were pooled. Each well was sequenced using a Miseq sequencer.individual_names_and_position.xlsx
DOI: 10.5061/dryad.n7m28
title: Data from: SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences

description: The recent advances in genome sequencing have revealed an abundance of
 non-synonymous polymorphisms among human individuals; subsequently, it is
 of immense interest and importance to predict whether such substitutions
 are functional neutral or have deleterious effects. The accuracy of such
 prediction algorithms depends on the quality of the multiple-sequence
 alignment, which is used to infer how an amino acid substitution is
 tolerated at a given position. Because of the scarcity of orthologous
 protein sequences in the past, the existing prediction algorithms all
 include sequences of protein paralogs in the alignment, which can dilute
 the conservation signal and affect prediction accuracy. However, we
 believe that, with the sequencing of a large number of mammalian genomes,
 it is now feasible to include only protein orthologs in the alignment and
 improve the prediction performance.
description: humanGenome_Results.part01hg19 predictions (part 1)humanGenome_Results.part02hg19 predictions (part 2)humanGenome_Results.part03hg19 predictions (part 3)humanGenome_Results.part04hg19 predictions (part 4)
DOI: 10.5061/dryad.vd61h
title: Data from: Open-ended song learning in a hummingbird

description: Vocal learning in birds is typically restricted to a sensitive period
 early in life, with the few exceptions to this rule reported in songbirds
 and parrots. Here we present evidence of open-ended vocal learning in a
 hummingbird, the third avian group with vocal learning. We studied
 vocalizations at four display leks of the long-billed hermit Phaethornis
 longirostris during a four-year period. Individuals produce a single song
 repertoire, although several song-types can coexist at a single lek. We
 found that nine of 49 birds recorded on multiple days (18%) changed their
 song-type between consecutive recordings. Three of these birds replaced
 song-types twice. Moreover, the earliest estimated age when song
 replacement occurred ranged from 186 to 547 days (mean= 307 days) and all
 nine birds who replaced song-types produced a crystallized song before
 replacement. The findings indicate that song-type replacement is distinct
 from an initial early learning sensitive period. As half of lekking males
 do not survive past the first year of life in this species, song learning
 may well be extended throughout the lifespan. This behavior would be
 convergent to vocal learning programs found in parrots and some songbirds.
description: Sound files
 1Recordings of
 long-billed hermit (Phaethornis longirostris) songs from La Selva Costa
 Rica, 2010-2013. FIrst subset from a total of four.Sound files
 2Recordings of
 long-billed hermit (Phaethornis longirostris) songs from La Selva Costa
 Rica, 2010-2013. Second subset from a total of four.Sound files
 3Recordings of
 long-billed hermit (Phaethornis longirostris) songs from La Selva Costa
 Rica, 2010-2013. Third subset from a total of four.Sound files
 4Recordings of
 long-billed hermit (Phaethornis longirostris) songs from La Selva Costa
 Rica, 2010-2013. Four subset from a total of four.Metadata from sound
 files-Open-ended song learning in a hummingbirdExcel data sheet
 describing the sound files associated with the paper "Open-ended song
 learning in a hummingbird". The column "file name" provides
 the name of the sound files (without file extension).Metadata fro sound
 files-Open-ended song learning in a
 hummingbird.xlsx
DOI: 10.5061/dryad.7r22vb1
title: Data from: Impact of winter enclosures on the gut bacterial microbiota of red deer in the Bavarian Forest National Park

description: High numbers of red deer (Cervus elaphus) pose a challenge for natural
 forests because of their high browsing intensities, especially during
 winter months. To mitigate this human–wildlife conflict, conservation
 management in Central Europe involves luring red deer into fenced
 winter-feeding sites. The supplementary diet provided in these so-called
 winter enclosures strongly differs from the natural diet of red deer.
 Dietary shifts, however, can lead to an imbalance of the gut microbiota,
 which could promote bacterial pathogens. Moreover, increased
 inter-individual contact in winter enclosures enhances the exchange of
 symbiotic but also pathogenic bacteria. In this study, we used
 high-throughput sequencing of the 16S rRNA gene in fecal samples of red
 deer inhabiting the Bavarian Forest National Park to investigate
 differences in the gut bacterial microbiota between individuals in winter
 enclosures and individuals that ranged freely in the forests in winter. We
 also investigated the occurrence of potential zoonotic bacterial pathogens
 in both study groups. Our results revealed that proportions of bacterial
 taxa, alpha- and beta-diversities, and relative abundances of amplicon
 sequence variants in the gut bacterial microbiota of the two groups
 differed. These differences were attributed to the enrichment of bacterial
 taxa involved in the digestion of the supplementary food and to different
 natural diets consumed before entering the winter enclosures. We detected
 sequences with high similarities to known red deer pathogens in both study
 groups, but their relative abundances were low, which suggests that the
 population of red deer of the National Park Bavarian Forest is healthy.
description: red_deer_microbiome_16S
DOI: 10.5061/dryad.r67hd7t
title: Data from: Modularity of genes involved in local adaptation to climate despite physical linkage

description: Background: Linkage among genes experiencing different selection pressures
 can make natural selection less efficient. Theory predicts that when local
 adaptation is driven by complex and non-covarying stresses, increased
 linkage is favored for alleles with similar pleiotropic effects, with
 increased recombination favored among alleles with contrasting pleiotropic
 effects. Here, we introduce a framework to test these predictions with a
 co-association network analysis, which clusters loci based on differing
 associations. We use this framework to study the genetic architecture of
 local adaptation to climate in lodgepole pine, Pinus contorta, based on
 associations with environments. Results: We identify many clusters of
 candidate genes and SNPs associated with distinct environments, including
 aspects of aridity and freezing, and discover low recombination rates
 among some candidate genes in different clusters. Only a few genes contain
 SNPs with effects on more than one distinct aspect of climate. There is
 limited correspondence between co-association networks and gene regulatory
 networks. We further show how associations with environmental principal
 components can lead to misinterpretation. Finally, simulations illustrate
 both benefits and caveats of co-association networks. Conclusions: Our
 results support the prediction that different selection pressures favor
 the evolution of distinct groups of genes, each associating with a
 different aspect of climate. But our results went against the prediction
 that loci experiencing different sources of selection would have high
 recombination among them. These results give new insight into evolutionary
 debates about the extent of modularity, pleiotropy, and linkage in the
 evolution of genetic architectures.
description: Data and analysis
 scriptsThis .zip file contains
 folders for reproducing the results, figures, and evaluations for the
 manuscript. Once unzipped, see the README file for more
 information.ModularityCodeDryad.zip
DOI: 10.5281/zenodo.18379715
title: Unique Property Reference Number (UPRN) indicator: 3-30-300 Measures (UPRN_6_1)

description: This indicator evaluates access to urban nature at the UPRN level using the "3-30-300" rule. It assesses whether a property meets three criteria: visibility of at least 3 trees, location within a neighbourhood with 30% tree canopy cover, and proximity (within 300 metres) to the nearest local green space.
DOI: 10.5061/dryad.r2k76
title: Data from: Gene expression and drought response in an invasive thistle

description: Though rapid phenotypic evolution has been observed in many invasive plant
 species, less is known about the associated genetic mechanisms. Some
 hypotheses invoke the evolution of trade-offs in resource allocation to
 explain phenotypic differences between the native and invaded ranges of a
 species. Alternately, invasive species may benefit from a generalist
 strategy and perform well in many environments. Identification of the
 molecular changes associated with successful invasions can offer clues
 regarding the mechanistic basis of such hypotheses, even in non-model
 organisms. To complement studies of phenotypic variation, we investigate
 gene expression during drought response that might underlie variation in
 drought tolerance between native and introduced populations of diffuse
 knapweed (Centaurea diffusa), and possibly contribute to invasion success.
 Using species-specific microarrays and tissue sampled under drought and
 control conditions at three time points, we identified genes whose
 expression either varied constitutively or responded to drought stress
 differently between ranges. Further, we functionally investigate these
 genes. Based on these data, invasive populations have constitutively
 higher levels of expression relating to energy production and lower levels
 of signal transduction expression relative to native populations. Under
 drought conditions, invasive populations may maintain energy production
 and react less strongly to drought than native populations, which may
 allow them to maintain fitness across moderate environmental variation.
 This supports the expectation of invasive populations consisting of
 generalist genotypes capable of fitness homeostasis, which may have
 facilitated the successful invasion of many environments in North America.
description: Supplementary tables and
 figuresCdiff_expression_supmat_BiolInv.docxTableS3_LRTsLRTsandTAIRaccessions.xlsxTableS5GOresults_DroughtGOresults_sigTrt_pc.xlsxPreprocessedMicroarrayDataknn_xys.zipFull_LRTs_ResultsCdifexprs_lme4dat.txtProcessedExpressionDataMatrixCdif_exprs_matrix.txtCode repositoryGithub repository storing R scripts used in this paper.Raw gene expression dataRawData_Cdifexprs.zip.gz
DOI: 10.5281/zenodo.18379714
title: Unique Property Reference Number (UPRN) indicator: 3-30-300 Measures (UPRN_6_1)

description: This indicator evaluates access to urban nature at the UPRN level using the "3-30-300" rule. It assesses whether a property meets three criteria: visibility of at least 3 trees, location within a neighbourhood with 30% tree canopy cover, and proximity (within 300 metres) to the nearest local green space.
DOI: 10.5061/dryad.4r8p3
title: Data from: When should species richness be energy limited, and how would we know?

description: Energetic constraints are fundamental to ecology and evolution, and
 empirical relationships between species richness and estimates of
 available energy (i.e. resources) have led some to suggest that richness
 is energetically constrained. However, the mechanism linking energy with
 richness is rarely specified and predictions of secondary patterns
 consistent with energy-constrained richness are lacking. Here, we lay out
 the necessary and sufficient assumptions of a causal relationship linking
 energy gradients to richness gradients. We then describe an
 eco-evolutionary simulation model that combines spatially explicit
 diversification with trait evolution, resource availability and
 assemblage-level carrying capacities. Our model identified patterns in
 richness and phylogenetic structure expected when a spatial gradient in
 energy availability determines the number of individuals supported in a
 given area. A comparison to patterns under alternative scenarios, in which
 fundamental assumptions behind energetic explanations were violated,
 revealed patterns that are useful for evaluating the importance of
 energetic constraints in empirical systems. We use a data set on rockfish
 (genus Sebastes) from the northeastern Pacific to show how empirical data
 can be coupled with model predictions to evaluate the role of energetic
 constraints in generating observed richness gradients.
description: READMERaw simulation results,
 no zero sum, tropical originno_zero_sum_tropical_sims.zipRaw simulation results, no zero sum, temperate originno_zero_sum_temperate_sims.zipRaw simulation results, zero sum, tropical origin, 1st of 2 fileszero_sum_tropical_sims_1_of_2.zipRaw simulation results, zero sum, tropical origin, 2nd of 2 fileszero_sum_tropical_sims_2_of_2.zipRaw simulation results, zero sum, temperate origin, 1st of 2 fileszero_sum_temperate_sims_1_of_2.zipRaw simulation results, zero sum, temperate origin, 2nd of 2 fileszero_sum_temperate_sims_2_of_2.zipSimulation analysis, no zero sum, tropical originno_zero_sum_tropical_analysis.zipSimulation analysis, no zero sum, temperate originno_zero_sum_temperate_analysis.zipSimulation analysis, zero sum, tropical originzero_sum_tropical_analysis.zipSimulation analysis, zero sum, temperate originzero_sum_temperate_analysis.zipPhylogenetic tree of genus SebastesObject of class 'phylo' described in Ingram, T. 2011. Speciation along a depth gradient in a marine adaptive radiation. Proc Roy Soc B: 278: 613-618. doi:10.1098/rspb.2010.1127Sebastes_tree_Ingram2011PRSB.phyDistributional data for Sebastes in the Northeast PacificLatitudinal ranges (and depth ranges) of species as compiled in Ingram, T. 2011. Speciation along a depth gradient in a marine adaptive radiation. Proc Roy Soc B: 278: 613-618. doi:10.1098/rspb.2010.1127Sebastes_distrib_data.csv
DOI: 10.5061/dryad.vm142
title: Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

description: Clonally reproducing plants have the potential to bear a significantly
 greater mutational load than sexually reproducing species. To investigate
 this possibility, we examined the breadth of genome-wide structural
 variation in a panel of monoploid/doubled monoploid clones generated from
 native populations of diploid potato (Solanum tuberosum), a highly
 heterozygous asexually propagated plant. As rare instances of purely
 homozygous clones, they provided an ideal set for determining the degree
 of structural variation tolerated by this species, and deriving its
 minimal gene complement. Extensive copy number variation (CNV) was
 uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30%
 of genes subject to at least partial duplication or deletion, revealing
 the highly heterogeneous nature of the potato genome. Dispensable genes
 (&gt;7,000) were associated with limited transcription and/or a recent
 evolutionary history, with lower deletion frequency observed in genes
 conserved across angiosperms. Association of CNV with plant adaptation was
 highlighted by enrichment in gene clusters encoding functions for
 environmental stress response, with gene duplication playing a part in
 species-specific expansions of stress-related gene families. This study
 revealed unique impacts of CNV in a species with asexual reproductive
 habits, and how CNV may drive adaption through evolution of key stress
 pathways.
description: less_than_85cov_85id_at_least_500_bp_removed_contamination_transcriptsM1_type_a_snps.hiconfM2_type_a_snps.hiconfM3_type_a_snps.hiconfM4_type_a_snps.hiconfM5_type_a_snps.hiconfM6_type_a_snps.hiconfM7_type_a_snps.hiconfM8_type_a_snps.hiconfM9_type_a_snps.hiconfM10_type_a_snps.hiconfM11_type_a_snps.hiconfM13_type_a_snps.hiconfDM_v4.04_assemblyContains 2 files: potato_dm_v404_all_pm_un.fasta and potato_dm_ChrUn.gff3
DOI: 10.5061/dryad.mr556
title: Data from: Hovering hummingbird wing aerodynamics during the annual cycle

description: The diverse hummingbird family (Trochilidae) has unique adaptations for
 nectarivory, among which is the ability to sustain hover-feeding. As
 hummingbirds mainly feed while hovering, it is crucial to maintain this
 ability throughout the annual cycle—especially during flight-feather
 moult, in which wing area is reduced. To quantify the aerodynamic
 characteristics and flow mechanisms of a hummingbird wing throughout the
 annual cycle, time-accurate aerodynamic loads and flow field measurements
 were correlated over a dynamically scaled wing model of Anna’s hummingbird
 (Calypte anna). We present measurements recorded over a model of a
 complete wing to evaluate the baseline aerodynamic characteristics and
 flow mechanisms. We found that the vorticity concentration that had
 developed from the wing’s leading-edge differs from the attached vorticity
 structure that was typically found over insects’ wings; firstly, it is
 more elongated along the wing chord, and secondly, it encounters high
 levels of fluctuations rather than a steady vortex. Lift characteristics
 resemble those of insects; however, a 20% increase in the lift-to-torque
 ratio was obtained for the hummingbird wing model. Time-accurate
 aerodynamic loads were also used to evaluate the time-evolution of the
 specific power required from the flight muscles, and the overall wingbeat
 power requirements nicely matched previous studies.
description: Aerodynamic
 loadsAerodynamic loads for
 all tested wingssecond_third_moment_butterFc_40_wInst_SurfaceArea9p12.matComplete wing chordwise z=0.25PIV measurements of the complete wing at z=0.25 at all tested angles of attackPIV_chordwise_full_z_0p25.matComplete wing chordwise z=0.5PIV measurements of the complete wing at z=0.5 at all tested angles of attackPIV_chordwise_full_z_0p50.matComplete wing chordwise z=0.75PIV measurements of the complete wing at z=0.75 at all tested angles of attackPIV_chordwise_full_z_0p75.matP1-4 wing chordwise z=0.25PIV measurements of the P1-4 wing at z=0.25 at all tested angles of attackPIV_chordwise_P1P2P3P4_z_0p25.matP1-4 wing chordwise z=0.5PIV measurements of the P1-4 wing at z=0.5 at all tested angles of attackPIV_chordwise_P1P2P3P4_z_0p50.matP10 wing chordwise z=0.5PIV measurements of the P10 wing at z=0.5 at all tested angles of attackPIV_chordwise_P10_z_0p50.matP10 wing chordwise z=0.75PIV measurements of the P10 wing at z=0.75 at all tested angles of attackPIV_chordwise_P10_z_0p75.matComplete wing spanwisePIV measurements of the complete wing at all tested angles of attackPIV_spanwise_full.matP1-4 wing spanwisePIV measurements of the P1-4 wing at all tested angles of attackPIV_spanwise_P1P2P3P4.matP89 wing spanwisePIV measurements of the P89 wing at all tested angles of attackPIV_spanwise_P8P9.mat
DOI: 10.5061/dryad.ht369
title: Data from: Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow

description: Mantel-based tests have been the primary analytical methods for
 understanding how landscape features influence observed spatial genetic
 structure. Simulation studies examining Mantel-based approaches have
 highlighted major challenges associated with the use of such tests and
 fueled debate on when the Mantel test is appropriate for landscape
 genetics studies. We aim to provide some clarity in this debate using
 spatially explicit, individual-based, genetic simulations to examine the
 effects of the following on the performance of Mantel-based methods: (1)
 landscape configuration, (2) spatial genetic nonequilibrium, (3) nonlinear
 relationships between genetic and cost distances, and (4) correlation
 among cost distances derived from competing resistance models. Under most
 conditions, Mantel-based methods performed poorly. Causal modeling
 identified the true model only 22% of the time. Using relative support and
 simple Mantel r values boosted performance to approximately 50%. Across
 all methods, performance increased when landscapes were more fragmented,
 spatial genetic equilibrium was reached, and the relationship between cost
 distance and genetic distance was linearized. Performance depended on cost
 distance correlations among resistance models rather than cell-wise
 resistance correlations. Given these results, we suggest that the use of
 Mantel tests with linearized relationships is appropriate for
 discriminating among resistance models that have cost distance
 correlations &lt;0.85 with each other for causal modeling, or
 &lt;0.95 for relative support or simple Mantel r. Because most
 alternative parameterizations of resistance for the same landscape
 variable will result in highly correlated cost distances, the use of
 Mantel test-based methods to fine-tune resistance values will often not be
 effective.
description: CDPOP_simulationoutput_files_PlaceholderCDPOP simulation output files for one replicate run of "truth" R100N50_10U and the corresponding cost-distance matrices.R100N50_10U_CDPOPoutput_cdmats.zipCDmatricesThis file contains all cost-distance matrices used in simulations and analyses.