cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.78dj7t9
title: Data from: Improved campephiline detection: an experiment conducted with the Magellanic woodpecker

description: 1. Woodpeckers can be difficult to detect, as they are often cryptic,
 secretive, occurring in low densities, and wary of humans. Several methods
 exist to detect woodpeckers (e.g., playback surveys, passive point
 counts), yet no research has established which technique best detects
 these elusive picids. Thus, we designed an experiment to determine which
 of three methods best results in a detection of Magellanic Woodpeckers
 (Campephilus magellanicus), and if weather variables influence detection
 probability. 2. Mostly during austral summers 2015-2017, we i) used a
 drumming device to simulate a double-knock (i.e., territorial acoustical
 signal), ii) broadcasted a territorial call, and iii) passively listened
 (control) for Magellanic Woodpeckers. We conducted our experiment on
 Navarino Island, Chile, where the Magellanic Woodpecker is the sole picid.
 3. The drumming device most effectively influenced the likelihood of a
 woodpecker detection. The odds of a woodpecker responding to a
 double-knock were 2.1 times more likely than responding to either a call
 or control. Moreover, the odds of a woodpecker detection decreased by 42%
 as wind increased by one category and decreased by 40% for every
 additional month (i.e., Oct.-Mar.), which was expected because woodpeckers
 become less territorial as the breeding season progresses. 4. As
 Campephilus woodpeckers communicate via drums or double-knocks, using a
 drumming device likely will be an effective technique to detect not only
 Magellanic Woodpeckers, but other woodpeckers within the Campephilus genus
 in Central and South America.
description: MAWORscriptALWThis file contains all of the R code used in RStudio for this manuscript. Notes have been added to the code for clarity.DE.allData in this file contain all Magellanic Woodpecker detections recorded within the 10-minute survey and were analyzed in RStudio. The file name is the same in the R code; however, this file is an xlsx extension (as opposed to csv) to retain formatting.First.DetectData in this file only contain the first Magellanic Woodpecker detection recorded within the 10-minute survey and were analyzed in RStudio. The file name is the same in the R code; however, this file is an xlsx extension (as opposed to csv) to retain formatting.
DOI: 10.5061/dryad.gd30977
title: Data from: Context-dependent consequences of colour biases in a social fish

description: Colourful visual signals can provide receivers with valuable information
 about food, danger, and the quality of social partners. However, the value
 of the information that colour provides varies depending on the situation,
 and colour may even act as a sensory trap where signals that evolved under
 one context are exploited in another. Despite some elegant early work on
 colour as a sensory trap, few empirical studies have examined how colour
 biases may vary depending on context and under which situations biases can
 be overridden. Here, using Neolamprologus pulcher, a highly social cichlid
 fish from Lake Tanganyika, we conducted a series of experiments to
 determine colour biases and investigate the effects of these biases under
 different contexts. We found that N. pulcher interacted the most with
 yellow items and the least with blue items. These biases were maintained
 during a foraging-based associative learning assay, with fish trained
 using yellow stimuli performing better than those trained using blue
 stimuli. However, these differences in learning performance did not extend
 to reversal learning; fish were equally capable of forming new
 associations regardless of the colour they were initially trained on.
 Finally, in a social choice assay, N. pulcher did not display a stronger
 preference for conspecifics whose yellow facial markings had been
 artificially enhanced. Together, these findings suggest that the influence
 of colour biases varies under different contexts and support the
 situational dependency of colour functions.
description: Data from the four experimental series described in
 "Context-dependent consequences of colour biases in a social
 fish".
DOI: 10.5061/dryad.93tf68k
title: Data from: Extra-pair mating in a passerine bird with highly duplicated MHC class II: Preference for the golden mean

description: Genes of the major histocompatibility complex (MHC) are essential in
 vertebrate adaptive immunity, and they are highly diverse and duplicated
 in many lineages. While it is widely established that pathogen-mediated
 selection maintains MHC diversity through balancing selection, the role of
 mate choice in shaping MHC diversity is debated. Here, we investigate
 female mating preferences for MHC class II (MHCII) in the bluethroat
 (Luscinia svecica), a passerine bird with high levels of extra-pair
 paternity and extremely duplicated MHCII. We genotyped family samples with
 mixed paternity and categorized their MHCII alleles according to their
 functional properties in peptide binding. Our results strongly indicate
 that females select extra-pair males in a non-random, self-matching manner
 that provides offspring with an allelic repertoire size closer to the
 population mean, as compared to offspring sired by the social male. This
 is consistent with a “compatible genes” model for extra-pair mate choice
 where the optimal allelic diversity is intermediate, not maximal. This
 “golden mean” presumably reflects a trade-off between maximizing pathogen
 recognition benefits and minimizing autoimmunity costs. Our study
 exemplifies how mate choice can reduce the population variance in
 individual MHC diversity and exert strong stabilizing selection on the
 trait. It also supports the hypothesis that extra-pair mating is adaptive
 through enhanced genetic quality of offspring.
description: Script_initial_filtering_RawData-to-jMHCinput Bash script for making the jMHC input file from the raw MiSeq data   R_scripts_Rekdal-et-al-2019 Scripts for the analyses conducted in R   README_explanation_files Explanations of the files deposited   inputfiles TAR archive file containing the input files for the analyses in R   output_simulations Output files generated from the simulations in R, which the statistics reported in the manuscript are based on
DOI: 10.5061/dryad.943mp78
title: Data from: Genetic divergence and phenotypic plasticity contribute to variation in cuticular hydrocarbons in the seaweed fly Coelopa frigida

description: Cuticular hydrocarbons (CHCs) form the boundary between insects and their
 environments and often act as essential cues for species, mate and kin
 recognition. This complex polygenic trait can be highly variable both
 among and within species, but the causes of this variation, especially the
 genetic basis, are largely unknown. In this study, we investigated
 phenotypic and genetic variation of CHCs in the seaweed fly, C. frigida,
 and found that composition was affected by both genetic (sex and
 population) and environmental (larval diet) factors. We subsequently
 conducted behavioral trials that show CHCs are likely used as a sexual
 signal. We identified general shifts in CHC chemistry as well as
 individual compounds and found that the methylated compounds, mean chain
 length, proportion of alkenes, and normalized total CHCs differed between
 sexes and populations. We combined this data with whole genome
 re-sequencing data to examine the genetic underpinnings of these
 differences. We identified 11 genes related to CHC synthesis and found
 population level outlier SNPs in 5 that are concordant with phenotypic
 differences. Together these results reveal that the CHC composition of C.
 frigida is dynamic, strongly affected by the larval environment, and
 likely under natural and sexual selection.
description: adult_frigidaThe transcriptome used in this study.Fly IDsInformation about all of the flies used in the GC-MS analysisFly_IDs.xlsxSex & population analysisRaw GC-MS output for the flies used in the sex and population analyses.Wrack type analysisRaw GC-MS data for the animals used in the wrack type/diet analysisGenomic transcriptsGenomic regions containing the candidate genes used in the FST analysis.chc_genomic_transcripts.fasta
DOI: 10.5061/dryad.j6v0fq0
title: Data from: Dynamic up- and down-regulation of the default (DMN) and extrinsic (EMN) mode networks during alternating task-on and task-off periods

description: Using fMRI, Hugdahl et al. (2015) reported the existence of a
 general-domain cortical network during active task-processing which was
 non-specific to the cognitive task being processed. They labelled this
 network the extrinsic mode network (EMN). The EMN would be predicted to be
 negatively, or anti-correlated with the classic default mode network
 (DMN), typically observed during periods of rest, such that while the EMN
 should be down-regulated and the DMN up-regulated in the absence of
 demands for task-processing, the reverse should occur when demands change
 from resting to task-processing. This would require alternating periods of
 task-processing and resting, and analyzing data continuously when demands
 change from active to passive periods and vice versa. We were particularly
 interested in how the networks interact in the critical transition points
 between conditions. For this purpose we used an auditory task with
 multiple cognitive demands in a standard fMRI block-design. Task-present
 (ON) blocks were alternated with an equal number of task-absent, or rest
 (OFF) blocks to capture network dynamics across time and changing
 environmental demands. To achieve this, we specified the onset of each
 block, and used a finite-impulse response function (FIR) as basis function
 for estimation of the fMRI-BOLD response. During active (ON) blocks, the
 results showed an initial rapid onset of activity in the EMN network,
 which remained throughout the period, and faded away during the first scan
 of the OFF-block. During OFF blocks, activity in the DMN network showed an
 initial time-lag where neither the EMN nor the DMN was active, after which
 the DMN was up-regulated. Studying network dynamics in alternating passive
 and active periods may provide new insights into brain network interaction
 and regulation.
description: EMN_DMN_DichoticListeningfMRI task-based data analysis performed in SPM. ZIP folder contains: Group level results (second level) files, including contrasts files. Further description in the README file
DOI: 10.5061/dryad.d39d356
title: Data from: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming

description: Understanding the degree to which plant communities are open to seedling
 recruitment is key to predicting how they will be impacted by climate
 change. We experimentally assessed whether communities assembled under
 colder climates were inherently more open to recruitment than
 warmer-climate communities, after controlling for differences in the
 current climate under which the communities were growing. We then tested
 whether variation in openness to recruitment could be explained by
 community biomass or by the plant functional traits of the community. The
 study was conducted in a climate grid of twelve grassland sites across
 southern Norway, differing systematically in temperature and
 precipitation. Along a 2000 mm precipitation gradient, we transplanted
 turfs with intact plant communities from alpine and sub-alpine sites into
 2℃ warmer sites, and measured natural seedling emergence in these
 transplanted turfs vs. locally replanted control turfs at the transplant
 destination sites. Mixed effect models were used to assess the effect of
 origin (cold vs warm climate), biomass, and functional trait composition
 of the communities on seedling emergence. We further assessed variation in
 these effects across different climatic contexts (the temperature and
 precipitation gradients). Communities originating from colder climates
 were consistently more open to recruitment, with on average 44% more
 seedlings emerging, than the locally replanted control communities. The
 higher rates of seedling emergence in colder-climate communities were
 attributable to systematic differences in plant functional traits, but not
 in biomass. The colder-climate communities were composed of species with
 smaller leaves and lower maximum plant heights; traits that may make these
 communities less effective at excluding new recruits. These trait-related
 responses were not significant in the warmest sites and did not very
 across the precipitation gradient. Our results suggest that alpine species
 lack the competitive effect traits required to make their communities
 resistant to invasion by novel competitors under climate change.
description: Dataset metadata and data dictionary for the data from the paper
 “Functional traits, not productivity, predict openness to seedling
 recruitment in alpine plant communities under climatic warming“
 See README file SEEDCLIM_TT_community opennes
 to recruitmant.traits.biomass_2009.2011_data.xlsx
DOI: 10.5061/dryad.4qf7168
title: Data from: The genetic factors of bilaterian evolution

description: The Cambrian explosion was a unique animal radiation ~540 million years
 ago that produced the full range of body plans across bilaterians. The
 genetic mechanisms underlying these events are unknown, leaving a
 fundamental question in evolutionary biology unanswered. Using large-scale
 comparative genomics and advanced orthology evaluation techniques, we
 identified 157 genes with bilaterian origin. Bilaterian innovations
 include the entire Nodal pathway, a key regulator of mesoderm development
 and left-right axis specification; components for nervous system
 development, including a suite of G protein-coupled receptors that control
 physiology and behaviour, the Robo-Slit midline repulsion system, and the
 neurotrophin signalling system; a high number of zinc finger transcription
 factors; and novel factors that previously escaped attention.
 Contradicting the current view, our study reveals that genes with
 bilaterian origin are robustly associated with key features in extant
 bilaterians, suggesting a causal relationship.
description: Sequence set used to
 create the BigWenDBThis file contains
 124,031,501 sequences (in fasta format) from 273 species. It has been used
 in the OrthoMCL orthology clustering pipeline to identify
 bilaterian-specific genes as described in our article "The genetic
 factors of bilaterian evolution". The md5sum of the file
 'all.orf.taxid.fa' is:
 199aa7b795c79442d6bce4aca28e699aall.orf.taxid.fa.gz824605 orthogroups and their ancestors and compositionThis file has 824605 lines and contains for every orthogroup obtained in the final clustering a description of its ancestor and phylogenetic composition. Orthogroup ID (mcl.ortho-coortho.1.3.7_ID) is in field 1 of each line, taxon ID and taxon name of inferred orthogroup ancestor populate fields 2 and 3, with the number of species belonging to the orthogroup in field 4. The following fields inform about the presence of larger taxa (such as Bilateria, Porifera, Metazoa etc.) and the corresponding number of species found in the orthogroup. Finally, all taxon IDs and the number of sequences belonging to that species are listed.gro_ortho-co_13_7_nTaxonomic lineage information for the 273 species used in this study.Tab-separated file containing lineage information for the 273 species represented in this study, according to NCBI taxonomy.table2name.tab
DOI: 10.5061/dryad.t6855h4
title: Data from: Gender disparity in physician authorship among commentary articles in high impact medical journals

description: Background: There is an attrition of women physicians in academic medicine
 hierarchy. Scholarship in medical journals plays a direct role in career
 advancement, promotion, and authoritative recognition, and women physician
 authors are underrepresented in original research articles. Objectives: We
 sought to determine if women physician authors are similarly
 underrepresented in commentary articles within high impact journals.
 Design/Setting/Participants: In this observational study, we abstracted
 gender, degree, and authorship position from January 1, 2014 to October
 16, 2018 among commentary articles in three high impact journals: 1) JAMA
 Viewpoint; 2) NEJM Perspective; and 3) Annals of Internal Medicine Ideas
 and Opinions. Primary Outcome Measure: To compare the percentages of
 authors by gender, degree, authorship position, and journal in commentary
 articles, and assess for trends over a five-year period. Secondary Outcome
 Measures: To compare the proportion of men and women physician authorship
 of commentaries relative to the proportion of men and women physician
 faculty within academic medicine. To examine the gender concordance
 between last and first authors. Results: Of the 2,087 articles during the
 study period, 48% were men physician first authors compared to 17% women
 physician first authors (p&lt;0.0001). Of the 1,477 articles with more
 than one author, similar distributions were found with regard to last
 authors: 55% were men physicians compared to only 12% of women physicians
 (p&lt;0.0001). The proportion of women physician first authors
 increased over time, however the proportion of women physician last
 authors remained stagnant. Women authors in the first and last position
 were concordant in 9% of articles, men authors in the first and last
 author position were concordant in 55% of articles. Conclusions: Women
 physician authors remain underrepresented in commentary articles compared
 to men physician authors in the first and last author position. The
 proportion of women first authors was lowest with a women last author.
description: allyearjournalcomparisonAuthors, their inferred gender, their degrees, and their authorship order by journal and date from 1/1/2014-10/16/2018
DOI: 10.5061/dryad.8gh0135
title: Data from: Sonar estimation of summer chum and pink salmon in the Anvik River, Alaska, 2018

description: Dual-frequency identification sonar (DIDSON) was used to estimate adult
 summer chum salmon Oncorhynchus keta and pink salmon O. gorbuscha passage
 in the Anvik River from June 15 to July 26, 2018. Apportionment to species
 was determined using data collected from tower counts. A total of 305,098
 (SE 5,926) summer chum and 1,122,346 (SE 7,588) pink salmon were estimated
 to have passed the sonar site. A beach seine sample fishery was conducted
 to collect age, sex, and length information. Both sonar systems functioned
 well with minimal interruptions to operation. Range of ensonification was
 considered adequate for most fish that migrated upstream.
description: 2018 Anvik River Summer
 Chum Salmon Estimates Summer chum salmon daily
 and cumulative passage estimates at the Anvik River sonar project,
 2018.     
 2018 Anvik River Pink
 Salmon Estimates Pink salmon daily and
 cumulative passage estimates at the Anvik River sonar project,
 2018.   
 2018 Anvik River Tower
 Counts Salmon species and
 proportion of summer chum salmon observed migrating upstream during tower
 counts by day and bank at the Anvik River sonar project, 2018.
  
 
 2018 Anvik River
 Climatic Observations Climatic observations
 recorded daily at 1600 hours at the Anvik River sonar project site,
 2018.   
 2018 Anvik River Water
 Temperature Daily water temperatures
 on the left bank at the Anvik River sonar project, 2018.
DOI: 10.5061/dryad.fk869rf
title: Data from: Model-based species delimitation: are coalescent species reproductively isolated?

description: A large and growing fraction of systematists define species as
 independently evolving lineages that may be recognized by analyzing the
 population genetic history of alleles sampled from individuals belonging
 to those species. This has motivated the development of increasingly
 sophisticated statistical models rooted in the multispecies coalescent
 process. Specifically, these models allow for simultaneous estimation of
 the number of species present in a sample of individuals and the
 phylogenetic history of those species using only DNA sequence data from
 independent loci. These methods hold extraordinary promise for increasing
 the efficiency of species discovery, but require extensive validation to
 ensure that they are accurate and precise. Whether the species identified
 by these methods correspond to the species that would be recognized by
 alternative species recognition criteria (such as measurements of
 reproductive isolation) is currently an open question, and a subject of
 vigorous debate. Here we perform an empirical test of these methods by
 making use of a classic model system in the history of speciation
 research, flies of the genus Drosophila. Specifically, we use the uniquely
 comprehensive data on reproductive isolation that is available for this
 system, along with DNA sequence data, to ask whether Drosophila species
 inferred under the multispecies coalescent model correspond to those
 recognized by many decades of speciation research. We found that
 coalescent based and reproductive isolation based methods of inferring
 species boundaries are concordant for 77% of the species pairs. We explore
 and discuss potential explanations for these discrepancies. We also found
 that the amount of prezygotic isolation between two species is a strong
 predictor of the posterior probability of species boundaries based on DNA
 sequence data, regardless of whether the species pairs are sympatrically
 or allopatrically distributed.
description: phylip_alignmentsMUSCLE aligned phylip files for each species group.phylip_alignment.zippython_R_scriptsCustom python and R scripts used to calculate PPIL value and parse MCMC output files.Supplementary_FiguresSupplementary figures S1-S8.bpp_output_MCMCOutput files from all bpp runs, includes standard bpp output files and MCMC output.Supplementary_TablesSupplementary Tables S1-S5.