cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.17k8j
title: Data from: Gene tree discordance causes apparent substitution rate variation

description: Substitution rates are known to be variable among genes, chromosomes,
 species, and lineages due to multifarious biological processes. Here, we
 consider another source of substitution rate variation due to a technical
 bias associated with gene tree discordance. Discordance has been found to
 be rampant in genome-wide data sets, often due to incomplete lineage
 sorting (ILS). This apparent substitution rate variation is caused when
 substitutions that occur on discordant gene trees are analyzed in the
 context of a single, fixed species tree. Such substitutions have to be
 resolved by proposing multiple substitutions on the species tree, and we
 therefore refer to this phenomenon as Substitutions Produced by ILS
 (SPILS). We use simulations to demonstrate that SPILS has a larger effect
 with increasing levels of ILS, and on trees with larger numbers of taxa.
 Specific branches of the species trees are consistently, but erroneously,
 inferred to be longer or shorter, and we show that these branches can be
 predicted based on discordant tree topologies. Moreover, we observe that
 fixing a species tree topology when performing tests of positive selection
 increases the false positive rate, particularly for genes whose discordant
 topologies are most affected by SPILS. Finally, we use data from multiple
 Drosophila species to show that SPILS can be detected in nature. Although
 the effects of SPILS are modest per gene, it has the potential to affect
 substitution rate variation whenever high levels of ILS are present,
 particularly in rapid radiations. The problems outlined here have
 implications for character mapping of any type of trait, and for any
 biological process that causes discordance. We discuss possible solutions
 to these problems, and areas in which they are likely to have caused
 faulty inferences of convergence and accelerated evolution.
description: alignments_trees.tarAlignments and phylogenetic trees of simulated DNA sequences and of Drosophila sequences from Larracuente A., Sackton T., Greenberg A., Wong A., Singh N., Sturgill D., Zhang Y., Oliver B., Clark A. 2008. Evolution of protein-coding genes in Drosophila. Trends in Genetics. 24:114–23.sup_fig1Supplementary figure 1.sup_fig2Supplementary figure 2.sup_fig3Supplementary figure 3.sup_fig4Supplementary figure 4.sup_fig5Supplementary figure 5.sup_fig6Supplementary figure 6.sup_fig_captionsSupplementary figure captions.
DOI: 10.5061/dryad.9p5hm
title: Data from: Male monkeys use punishment and coercion to de-escalate costly intergroup fights

description: In numerous social species, males direct aggression towards female group
 members during intergroup fights, and this behaviour is commonly thought
 to function as mate guarding, even though males often target non-receptive
 females. In studying intergroup fights in a wild population of vervet
 monkeys, we found that male intragroup aggression was primarily directed
 towards individuals who had either just finished exhibiting, or were
 currently attempting to instigate intergroup aggression. Targeted females
 were less likely to instigate intergroup aggression in the future,
 indicating that male intragroup aggression functioned as coercion (when
 directed towards those who were currently trying to instigate a fight) and
 punishment (when directed towards those who had recently fought). These
 manipulative tactics effectively prevented intergroup encounters from
 escalating into fights and often de-escalated ongoing conflicts. Males who
 were likely sires were those most likely to use punishment/coercion,
 particularly when they were wounded, and therefore less able to protect
 vulnerable offspring should a risky intergroup fight erupt. This work,
 along with our previous finding that females use punishment and rewards to
 recruit males into participating in intergroup fights, highlights the
 inherent conflict of interest that exists between the sexes, as well as
 the role that social incentives can play in resolving this conflict.
 Furthermore, unlike other studies which have found punishment to be used
 asymmetrically between partners, these works represent a novel example of
 reciprocal punishment in a non-human animal.
description: Dataset_Seasonal
 Variability in Male Intragroup Social Interactions during Intergroup
 ConflictsDataset for GLMMs
 included in ESM, table s1, as well in the GLMM examining the co-occurrence
 of male and female social incentives.ProcRoySoc_Dataset_SeasonalVariab.csvProportion of cases targets instigated/participated in intergroup aggression before and after being aggressed, and baselineProportion of cases each targeted female had participated in the most recent instigating/aggressive episodes before being attacked by a male group member, proportion of cases they participated in next instigating/aggressive episode, and their personal baseline likelihood of participating in two consecutive episodes.ProcRoySoc_Before_After_Baseline_Targets.csvMovie of male intragroup aggression during a simulated intergroup encounterNote that in this example, the targeted female was not clearly instigating intergroup aggression, but was merely approaching the simulated intruders.Movie.avi
DOI: 10.5061/dryad.qk300
title: Data from: Coral snakes predict the evolution of mimicry across New World snakes

description: Batesian mimicry, in which harmless species (mimics) deter predators by
 deceitfully imitating the warning signals of noxious species (models),
 generates striking cases of phenotypic convergence that are classic
 examples of evolution by natural selection. However, mimicry of venomous
 coral snakes has remained controversial because of unresolved conflict
 between the predictions of mimicry theory and empirical patterns in the
 distribution and abundance of snakes. Here we integrate distributional,
 phenotypic and phylogenetic data across all New World snake species to
 demonstrate that shifts to mimetic coloration in nonvenomous snakes are
 highly correlated with coral snakes in both space and time, providing
 overwhelming support for Batesian mimicry. We also find that bidirectional
 transitions between mimetic and cryptic coloration are unexpectedly
 frequent over both long- and short-time scales, challenging traditional
 views of mimicry as a stable evolutionary ‘end point’ and suggesting that
 insect and snake mimicry may have different evolutionary dynamics.
description: Spatial data range map
 construction filesThis file contains all
 the shape files, and all scripts for their generation, for all species of
 New World snakes analysed in this manuscriptforDryad.zip
DOI: 10.5061/dryad.1641mj3
title: Data from: Improving conservation effectiveness of nature reserve for golden snub-nosed monkey, a niche-based approach

description: Reserve selections are often opportunistic rather than strategic and
 coordinated, and consequently many reserves are ineffective to achieve
 their intended goals of conservation. Here we assessed the conservation
 effectiveness of a reserve for the golden snub-nosed monkeys
 (Rhinopithecus roxellana) with a niche-based approach. We assessed habitat
 usage of the monkeys in Shennongjia Nature Reserve (SNR) and attributes of
 14 environmental variables that could potentially affect the monkeys’
 habitat use. Spatial distribution of potentially suitable habitat for the
 monkeys was then modeled with Maxent, a niche-based model, and
 conservation effectiveness of SNR was assessed by comparing the current
 boundary of the reserve with the spatial distribution of the modeled
 potential habitat and the current habitat area of the monkeys. Only 59% of
 the habitat area and 61% of the predicted potential habitat area were
 under the protection of SNR. To improve conservation effectiveness of SNR,
 we proposed that the current SNR be enlarged by 270 km2. The enlarged
 reserve would encompass 100% of the existing habitat area plus 89% of the
 predicted potential habitat area. Using the niche-based approach, we were
 able to integrate habitat usage data of the target species with that of
 remote sensing to identify areas potentially suitable as habitat for the
 species. This information not only can be used for improving conservation
 effectiveness of existing reserves but also for the effective planning and
 designing of new reserves.
description: basicdatainformation collected in the filed, simulated electronically.
DOI: 10.5061/dryad.n66h4
title: Data from: An exceptionally preserved Late Devonian actinopterygian provides a new model for primitive cranial anatomy in ray-finned fishes

description: Actinopterygians (ray-finned fishes) are the most diverse living
 osteichthyan (bony vertebrate) group, with a rich fossil record. However,
 details of their earliest history during the middle Palaeozoic (Devonian)
 ‘Age of Fishes' remains sketchy. This stems from an uneven
 understanding of anatomy in early actinopterygians, with a few well-known
 species dominating perceptions of primitive conditions. Here we present an
 exceptionally preserved ray-finned fish from the Late Devonian (Middle
 Frasnian, ca 373 Ma) of Pas-de-Calais, northern France. This new genus is
 represented by a single, three-dimensionally preserved skull. CT scanning
 reveals the presence of an almost complete braincase along with near-fully
 articulated mandibular, hyoid and gill arches. The neurocranium differs
 from the coeval Mimipiscis in displaying a short aortic canal with a
 distinct posterior notch, long grooves for the lateral dorsal aortae,
 large vestibular fontanelles and a broad postorbital process.
 Identification of similar but previously unrecognized features in other
 Devonian actinopterygians suggests that aspects of braincase anatomy in
 Mimipiscis are apomorphic, questioning its ubiquity as stand-in for
 generalized actinopterygian conditions. However, the gill skeleton of the
 new form broadly corresponds to that of Mimipiscis, and adds to an
 emerging picture of primitive branchial architecture in crown
 gnathostomes. The new genus is recovered in a polytomy with Mimiidae and a
 subset of Devonian and stratigraphically younger actinopterygians, with no
 support found for a monophyletic grouping of Moythomasia with Mimiidae.
description: Giles_et_al_2015_actinopts matrixData matrix for phylogenetic analysisGiles_et_al_2015_actinopts.nxBraincase and skull roof3D PLY file of braincase and skull roof.Braincase low res.plyGill skeleton3D PLY file of the gill skeleton.Endocast3D PLY file of the endocast.French_Fish_High_Res_Current_Endocast 3_001.plyWhole fossil3D PLY file of the whole fossil, excluding the braincase.
DOI: 10.5061/dryad.8k7jd
title: Data from: Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera

description: Background: The cyclic peptide toxins of Amanita mushrooms, such as
 α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and
 ribosomally biosynthesized. Based on partial genome sequence and PCR
 analysis, some members of the MSDIN family were previously identified in
 Amanita bisporigera, and several other members are known from other
 species of Amanita. However, the complete complement in any one species,
 and hence the genetic capacity for these fungi to make cyclic peptides,
 remains unknown. Results: Draft genome sequences of two cyclic
 peptide-producing mushrooms, the “Death Cap” A. phalloides and the
 “Destroying Angel” A. bisporigera, were obtained. Each species has ~30
 MSDIN genes, most of which are predicted to encode unknown cyclic
 peptides. Some MSDIN genes were duplicated in one or the other species,
 but only three were common to both species. A gene encoding cycloamanide
 B, a previously described nontoxic cyclic heptapeptide, was also present
 in A. phalloides, but genes for antamanide and cycloamanides A, C, and D
 were not. In A. bisporigera, RNA expression was observed for 20 of the
 MSDIN family members. Based on their predicted sequences, novel cyclic
 peptides were searched for by LC/MS/MS in extracts of A. phalloides. The
 presence of two cyclic peptides, named cycloamanides E and F with
 structures cyclo(SFFFPVP) and cyclo(IVGILGLP), was thereby demonstrated.
 Of the MSDIN genes reported earlier from another specimen of A.
 bisporigera, 9 of 14 were not found in the current genome assembly.
 Differences between previous and current results for the complement of
 MSDIN genes and cyclic peptides in the two fungi probably represents
 natural variation among geographically dispersed isolates of A. phalloides
 and among the members of the poorly defined A. bisporigera species
 complex. Both A. phalloides and A. bisporigera contain two prolyl
 oligopeptidase genes, one of which (POPB) is probably dedicated to cyclic
 peptide biosynthesis as it is in Galerina marginata. Conclusion: The MSDIN
 gene family has expanded and diverged rapidly in Amanita section
 Phalloideae. Together, A. bisporigera and A. phalloides are predicted to
 have the capacity to make more than 50 cyclic hexa-, hepta-, octa-, nona-
 and decapeptides.
description: Amanita_phalloides_Amanita_bisporigera_genome_annotation.tarThis tarball contains the following files: A_bisporigera_functional_annotation.txt A_bisporigera_predicted_proteins.fasta A_bisporigera_predicted_transcripts.fasta A_bisporigera_v1_genome_assembly.fasta A_bisporigera_v1_w_fasta.gff A_phalloides_functional_annotation.txt A_phalloides_predicted_proteins.fasta A_phalloides_predicted_transcripts.fasta A_phalloides_v1_genome_assembly.fasta A_phalloides_v1_w_fasta.gff
DOI: 10.5061/dryad.6c605
title: Data from: The Parmotrema acid test: a look at species delineation in the P. perforatum group 40 y later

description: Parmotrema perforatum and its relatives form a morphologically distinctive
 group of species, most of which are common and endemic to eastern North
 America. Species delimitation in this ecologically important group was the
 subject of extensive inquiry before the advent of molecular systematics
 and computationally intensive niche modeling. As part of a large-scale
 lichen biodiversity inventory of the Mid-Atlantic Coastal Plain, we used
 ITS sequence data to examine the utility of characters (morphological,
 chemical, reproductive, ecological) in circumscribing four species in this
 group (P. hypoleucinum, P. hypotropum, P. perforatum, P. subrigidum). We
 found that P. hypoleucinum and P. subrigidum as currently circumscribed
 are monophyletic and the latter comprises two chemotypes differing in the
 presence or absence of norstictic acid in addition to alectoronic acid.
 The sequences of P. hypotropum and P. perforatum, which are chemically
 identical species and differ only in reproductive mode, were intermixed in
 a single, well-supported clade. The two chemotypes of P. subrigidum are
 partially allopatric and their sequences are &gt; 99% identical.
 Nonetheless, niche modeling suggests they occupy significantly different
 ecological niches. These results provide a new perspective on much-debated
 questions on species circumscription in lichens and suggest new avenues
 for genetic, ecological and systematic research.
description: Modeling and molecular
 datasets for Parmotrema perforatum studyThe data packet is a
 zipped folder that contains 1) a folder with all relevant Maxent modeling
 files including a ReadMe and 2) a folder with four input files used for
 molecular phylogenetic analyses conducted as part of the
 study.Parmotrema_DatatoDeposit.zip
DOI: 10.15468/dl.x7ngz9
title: Occurrence Download

description: A dataset containing 425612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-12-01",
 "EventDate is less than or equal to 2025-12-31",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 425612 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000383-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3118j
title: Data from: Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

description: High-throughput phenotyping produces multiple measurements over time,
 which require new methods of analyses that are flexible in their
 quantification of plant growth and transpiration, yet are computationally
 economic. Here we develop such analyses and apply this to a rice
 population genotyped with a 700k SNP high-density array. Two rice
 diversity panels, indica and aus, containing a total of 553 genotypes, are
 phenotyped in waterlogged conditions. Using cubic smoothing splines to
 estimate plant growth and transpiration, we identify four time intervals
 that characterize the early responses of rice to salinity. Relative growth
 rate, transpiration rate and transpiration use efficiency (TUE) are
 analysed using a new association model that takes into account the
 interaction between treatment (control and salt) and genetic marker. This
 model allows the identification of previously undetected loci affecting
 TUE on chromosome 11, providing insights into the early responses of rice
 to salinity, in particular into the effects of salinity on plant growth
 and transpiration.
description: Data and scripts for
 data preparation and phenotypic analysisThe zip file contains
 the data and code files that were used in the data preparation and
 phenotypic analysis phases for the two rice experiments reported Al-Tamimi
 et al.: experiment 0254 that investigates an indica panel and experiment
 0255 that investigates an aus panel.Phenotyping_data_and_scripts.zipData and scripts for GWASThe zip file contains the data and code files that were used in the genome wide association study (GWAS) phase for the two experiments reported by Al-Tamimi et al.: experiment 0254 that investigates an indica panel and experiment 0255 that investigates an aus panel. In addition, the combined panel (INDAUS) was subject to a GWAS.GWAS_data_and_scripts.zipimageData: an R package that aids in processing and plotting data from a Lemna-Tec ScananalyzerThe R package imageData extracts traits from imaging data produced using a Lemna-Tec Scananalyzer. Growth rates between successive imagings are obtained and those for a nominated set of intervals can also be calculated. Profile or longitudinal plots of the traits and growth rates can be produced. It is available at http://cran.at.r-project.org/web/packages/imageData/index.html.
DOI: 10.5061/dryad.974k0
title: Data from: How can we get close to zero?: the potential contribution of biomedical prevention and the investment framework towards an effective response to HIV

description: Background: In 2011 an Investment Framework was proposed that described
 how the scale-up of key HIV interventions could dramatically reduce new
 HIV infections and deaths in low and middle income countries by 2015. This
 framework included ambitious coverage goals for prevention and treatment
 services resulting in a reduction of new HIV infections by more than half.
 However, it also estimated a leveling in the number of new infections at
 about 1 million annually after 2015. Methods: We modeled how the response
 to AIDS can be further expanded by scaling up antiretroviral treatment
 (ART) within the framework provided by the 2013 WHO treatment guidelines.
 We further explored the potential contributions of new prevention
 technologies: ‘Test and Treat’, pre-exposure prophylaxis and an HIV
 vaccine. Findings: Immediate aggressive scale up of existing approaches
 including the 2013 WHO guidelines could reduce new infections by 80%. A
 ‘Test and Treat’ approach could further reduce new infections. This could
 be further enhanced by a future highly effective pre-exposure prophylaxis
 and an HIV vaccine, so that a combination of all four approaches could
 reduce new infections to as low as 80,000 per year by 2050 and annual AIDS
 deaths to 260,000. Interpretation: In a set of ambitious scenarios, we
 find that immediate implementation of the 2013 WHO antiretroviral therapy
 guidelines could reduce new HIV infections by 80%. Further reductions may
 be achieved by moving to a ‘Test and Treat’ approach, and eventually by
 adding a highly effective pre-exposure prophylaxis and an HIV vaccine, if
 they become available.
description: Model output by country
 and indicatorThis Excel file contains
 the output of the model for each of the countries by indicator and
 year.NPT
 Results By Country-1-27-2014.xlsxGoals_Country_FilesThis is a compressed file that contains the Spectrum Goals files for the 23 countries that have been modeled. Each country file is also a compressed file with the extension PJNZ. These files can be opened with the Spectrum program.
DOI: 10.60520/ieda/114187
title: LA-ICP-MS settings for trace element analysis of volcanic glass at University of Cologne - v1

description: ICP:MS-LA instrument (University of Cologne) settings V1 applied to analyze volcanic glass fragments of tephra layers.
DOI: 10.5061/dryad.d1dp3h8
title: Data from: The distribution of income is worse than you think: including pollution impacts into measures of income inequality

description: This paper calculates the distribution of an adjusted measure of income
 that deducts damages due to exposure to air pollution from reported market
 income in the United States from 2011 to 2014. The Gini coefficient for
 this measure of adjusted income is 0.682 in 2011, as compared to 0.482 for
 market income. By 2014, we estimate that the Gini for adjusted income fell
 to 0.646, while the market income Gini did not appreciably change. The
 inclusion of air pollution damage acts like a regressive tax: with air
 pollution, the bottom 20% of households lose roughly 10% of the share of
 income, while the top 20% of households gain 10%. We find that, unlike the
 case for market income, New England is not the most unequal division with
 respect to adjusted income. Further, the difference between adjusted
 income for white and Hispanics is smaller than expected. However, the gap
 in augmented income between whites and African-Americans is widening.
description: Data_MMWG_PLOS_One_2018This directory contains income data, pollution levels, and vital statistics necessary to replicate the paper's findings. Data used in the paper for household income are publicly available at IPUMS-CPS , and are made available here with permission from IPUMS. Any subsequent use of these data should please cite IPUMS. For full citation, please see the attached README file.Scripts_MMWG_PLOS_One_2018This directory contains the Stata scripts necessary to replicate the results in the paper. It also contains a README file to instruct users on how to replicate. Data for household income used in the paper are publicly available at IPUMS-CPS and are made available here with permission from IPUMS. Any subsequent use of these data should please cite IPUMS. For full citation, please see the attached README file.