cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fs6kv67
title: Data from: ‘Keep the line moving’: residual system state potential as a baseball hitting-style indicator

description: The sport of baseball has a strong tradition of utilizing
 forward-projecting probabilistic measures, such as batting average, for
 performance assessment. Albeit highly informative and quite accurate, such
 measure of batting probability merely looks at how a player can
 probabilistically act upon the system in a forward manner, based on how
 they have acted upon that system in the past, but does not provide
 information about the state of the system itself once a player completes
 an at-bat. The current paper proposes a statistic called the Residual Run
 Potential Index (RRPI) as a measure of the ‘residual system state’ as it
 remains after a completed at bat. Derived from Retrosheet (2017) event
 data, the RRPI reflects a system-efficiency measure of player hitting
 style that retains maximized runscoring potential of the system state.
 RRPI calculations derived from a proprietary software simulation
 experiment, as well as for several Major League Baseball (MLB)
 Hall-of-Fame players, are also presented.
description: SARBB SIM data
 (Dryad)Microsoft Access raw
 data file. Raw statistical data generated by the Stat-A-Rama proprietary
 baseball simulation application during the 162 game
 simulation.RRPI data
 (Dryad)This Excel data file
 contains: [1] Compiled aggregate batting and pitching statistics for the
 Stat-A-Rama 162 game simulation [2] Win/Loss matchup data for the
 simulation [3] Pitching and batting data by game for the simulation [4]
 Linescores for all 162 games of the simulation [5] Raw residual base-state
 data as generated after each at-bat for the 162 game simulation [6]
 Simulation vs Real ARRP and RRPI values as complied for each player
 utilized during the 162 game simulation [7] RRPI calculation tool and
 instructions
DOI: 10.5061/dryad.032cq64
title: Data from: Skeletal microstructure of Stenopterygius quadriscissus (Reptilia, Ichthyosauria) from the Posidonienschiefer (Posidonia Shale, Lower Jurassic) of Germany

description: Ichthyosaurians (Ichthyosauria) are a major clade of secondarily aquatic
 marine tetrapods that occupied several major predatory niches during the
 Mesozoic Era. Multiple lines of evidence including isotopic, body shape
 and swimming modality analyses suggest they exhibited elevated growth and
 metabolic rates, and body temperatures. However, applications of
 osteohistological methods to test hypotheses regarding their physiology
 are few. Previous studies focused on the humeri, vertebrae and ribs from a
 small number of taxa. Here, we use osteohistological methods to describe
 the bone microstructure of over 30 cranial and post-cranial elements from
 a nearly complete, articulated individual of Stenopterygius quadriscissus
 from the Posidonienschiefer Formation (Posidonia Shale, Lower Jurassic) of
 Germany. The specimen shows highly vascularized primary bone and spongious
 secondary bone in its limbs, suggesting an overall shift to a lighter
 spongious structured skeleton was achieved through multiple developmental
 mechanisms. The modified perichondral ossification in elements of the
 limbs distal to the stylopodium informs our understanding of functional
 morphology, including hydrodynamic forces on the paddles. The ribs show
 variation in cortical thickness and trabecular organization along their
 length. Cyclical growth is inferred from changes in vascularization and
 osteocyte density as well as the presence of annuli in primary
 fibrolamellar bone. Cranial elements, due to their relative density and
 better preservation of growth marks, may prove to be of particular
 importance in future skeletochronological studies of post-Triassic
 ichthyosaurians. We infer and corroborate hypotheses of elevated growth
 rates and metabolic rates in ichthyosaurians, and the potential for
 thermoregulation similar to extant homeothermic ectotherms.
description: PALA-03-18-4179-OA-R2
 Supp Figs
DOI: 10.5061/dryad.1kk02qr
title: Data from: OpenNahele: the open Hawaiian forest plot database

description: This data paper provides a description of OpenNahele, the open Hawaiian
 forest plot database. OpenNahele includes 530 forest plots across the
 Hawaiian archipelago containing 43,590 individuals of 185 native and alien
 tree, shrub and tree fern species across six islands. We include estimates
 of maximum plant size (D950.1 and Dmax3) for 58 woody plant species, a key
 functional trait associated with dispersal distance and competition for
 light. OpenNahele can serve as a platform to test key ecological,
 evolutionary and conservation questions in a hotspot archipelago.
description: OpenNahele forest plot
 dataDiameter at breast
 height (or occurrence) of individual trees, shrubs, and tree ferns across
 530 plots across the Hawaiian archipelago and includes native status and
 cultivated status of the 185 species.OpenNahele_Tree_Data.csvOpenNahele Maximum Plant SizeMaximum plant size of 58 tree, shrub, and tree fern species that occur in 530 forest plots across the Hawaiian archipelago. Maximum plant size was estimated as D950.1and Dmax3 following King et al. (2006).OpenNahele_MaximumPlantSize.csv
DOI: 10.5061/dryad.79928sj
title: Data from: Rapid establishment of a flowering cline in Medicago polymorpha after invasion of North America

description: To establish and spread in a new location, an invasive species must be
 able to carry out its life cycle in novel environmental conditions. A key
 trait underlying fitness is the shift from vegetative to reproductive
 growth through floral development. In this study, we used a common garden
 experiment and genotyping-by-sequencing to test whether the latitudinal
 flowering cline of the North American invasive plant Medicago polymorpha
 was translocated from its European native range through multiple
 introductions, or whether the cline rapidly established due to evolution
 following a genetic bottleneck. Analysis of flowering time in 736 common
 garden plants showed a latitudinal flowering time cline in both the native
 and invaded ranges where genotypes from lower latitudes flowered earlier.
 Genotyping-by-sequencing of 9,658 SNPs in 446 individuals revealed two
 major subpopulations of M. polymorpha in the native range, only one of
 which is present in the invaded range. Additionally, native range
 populations have higher genetic diversity than invaded range populations,
 suggesting that a genetic bottleneck occurred during invasion. All invaded
 range individuals are closely related to plants collected from native
 range populations in Portugal and southern Spain, and population
 assignment tests assigned invaded range individuals to this same narrow
 source region. Taken together, our results suggest that latitudinal clinal
 variation in flowering time has rapidly evolved across the invaded range
 despite a genetic bottleneck following introduction.
description: SNP data for full GBS
 population of Medicago polymorphaThis file contains all
 SNP data for the full GBS population, as referenced in the publication.
 1st column: assigns individuals to the deep GBS population (denoted by 1)
 2nd column: Lists the unique IDs for each individual. In the deep GBS
 collection, N or I refers to Native or Invaded; followed by the
 three-letter population designation, and the five-digit ID. 3rd through N
 column: Designates the diploid alleles for each locus. 1=A, 2=C, 3=G, and
 4=T. 0 indicates NA, or no data.Mpol_wUSDA_original.csvMpolymorpha_FloweringTimeDataThis file describes the time until first flowering of each M. polymorpha individual in our common garden experiment, along with other associated data including the latitude and longitudinal coordinates of origin, the population, and whether or not the individual was included in the genotyping by sequencing study. It is noted that this file contains all of the individuals included in our common garden experiment, and individuals later determined to be a relative of M. polymorpha are indicated.FloweringTimeData.csv
DOI: 10.5061/dryad.1924
title: Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

description: Gene expression divergence is one of the mechanisms thought to be involved
 in the emergence of incipient species. Next-generation sequencing has
 become an extremely valuable tool for the study of this process by
 allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a
 454 GS-FLX pyrosequencing experiment in order to refine our understanding
 of adaptive divergence between dwarf and normal lake whitefish species
 (Coregonus clupeaformis spp.). The objectives were to: (1) investigate
 transcriptomic divergence as measured by liver RNA-Seq; (2) test the
 correlation between divergence in expression and sequence polymorphism and
 (3) investigate the extent of allelic imbalance. We also compared the
 results of RNA-seq with those of a previous microarray study performed on
 the same fish. Following de novo assembly, results showed that normal
 whitefish over-expressed more contigs associated with protein synthesis
 while dwarf fish over-expressed more contigs related to energy metabolism,
 immunity and DNA replication and repair. Moreover, 63 SNPs showed
 significant allelic imbalance, and this phenomenon prevailed in the
 recently diverged dwarf whitefish. Results also showed an absence of
 correlation between gene expression divergence as measured by RNA-Seq and
 either polymorphism rate or sequence divergence between normal and dwarf
 whitefish. This study reiterates an important role for gene expression
 divergence, and provides evidence for allele-specific expression
 divergence as well as evolutionary decoupling of regulatory and coding
 sequences in the adaptive divergence of normal and dwarf whitefish. It
 also demonstrates how next-generation sequencing can lead to a more
 comprehensive understanding of transcriptomic divergence in a young
 species pair.
description: De novo contigs from
 RNA-Seq of the whitefish liver transcriptomeExcel spreadsheet with
 de novo contigs from RNA-Seq of the whitefish liver transcriptome. Contig
 consensus sequences and gene expression values (RPKM) for dwarf and normal
 whitefish are presented.Supporting Information for
 online publication only_TS2.xls
DOI: 10.5061/dryad.f5g2482
title: Data from: Phylogenomics, life history and morphological evolution of ophiocomid brittlestars

description: Brittlestars in the family Ophiocomidae are large and colourful
 inhabitants of tropical shallow water habitats across the globe. Here we
 use targeted capture and next-generation sequencing to generate robust
 phylogenomic trees for 39 of the 43 species in order to test the monophyly
 of existing genera. The large genus Ophiocoma, as currently constituted,
 is paraphyletic on our trees and required revision. Four genera are
 recognised herein: an expanded Ophiomastix (now including Ophiocoma
 wendtii, O. occidentalis, O. endeani, O. macroplaca, and Ophiarthrum spp),
 Ophiocomella (now including the non-fissiparous Ophiocoma pumila, aethiops
 and valenciae) and Breviturma (now including Ophiocoma pica, O. pusilla,
 O. paucigranulata and O. longispina) and a restricted Ophiocoma. The
 resulting junior homonym Ophiomastix elegans is renamed O. brocki. The
 genus Ophiomastix exhibits relatively high rates of morphological
 disparity compared to other lineages. Ophiomastix flaccida and O.
 (formerly Ophiarthrum) pictum have divergent mitochondrial genomes,
 characterised by gene-order rearrangements, strand recoding, enriched GT
 base composition, and a corresponding divergence of nuclear mitochondrial
 protein genes. The new phylogeny indicates that larval and developmental
 transitions occurred rarely. Larval culture trials show that species with
 abbreviated lecithotrophic larval development occur only within
 Ophiomastix, although the possible monophyly of these species is obscured
 by the rapid early radiation within this genus. Asexual reproduction by
 fission is limited to one species-complex within Ophiocomella, also
 characterised by elevated levels of allelic heterozygosity, and which has
 achieved a relatively rapid global distribution. The crown ages of the new
 genera considerably predate the closure of the Tethyan seaway and all four
 are distributed in both the Atlantic and Indo-Pacific Oceans. Two species
 pairs appear to reflect the closure of the Panama Seaway, although their
 fossil-calibrated node ages (12–14 ± 6 my), derived from both concatenated
 sequence and multispecies coalescent analyses, considerably predate the
 terminal closure event. Ophiocoma erinaceus has crossed the East Pacific
 barrier and is recorded from Clipperton Island, SW of Mexico.
description: phylogenetic_dataStarBEAST_exonsZipped folder with 100 phased allele exon dataEC_pipelineZipped folder with exon-capture Unix shell scriptsGene_Table_v3Microsoft Excel file containing information on exon-capture target (genes and exons)Ophiocomid_Dryad_ReadMe_v1Information on files in this Dryad packageOphiocomid_Dryad_ReadMe_v2.docx
DOI: 10.5061/dryad.nk43478
title: Data from: Kinetics and mechanism of selenate and selenite removal in solution by sulfate-green rust

description: This work investigated the removal of selenite and selenate from water by
 sulfate-green rust (GR). Selenite was immobilized by simple adsorption
 onto GR at pH 8, and by adsorption-reduction at pH 9. Selenate was
 immobilized by adsorption-reduction to selenite and Se0 at both pH 8 and
 9. In the process, GR oxidized to goethite and magnetite. The removal of
 selenite and selenate by GR was kinetically described through a
 pseudo-second order model based on inductively-coupled plasma spectrometry
 (ICP) results. XAFS analysis enabled to elucidate the concentration
 profiles of Se and Fe species in the solid phase and allowed to
 distinguish two removal mechanism, namely adsorption and reduction.
 Selenite and selenate were reduced by GR through homogeneous solid-phase
 reaction upon adsorption and by heterogeneous reaction at the solid-liquid
 interface. The selenite reduced through heterogeneous reduction with GR
 was adsorbed onto GR but not reduced further. The redox reaction between
 GR and selenite/selenate was kinetically described through an irreversible
 second order bimolecular reaction model based on XAFS concentration
 profiles. Although the redox reaction became faster at pH 9, simple
 adsorption was always the fastest removal mechanism.
description: RSOR_data
DOI: 10.5061/dryad.8mb5r88
title: Data from: Augmented reality powers a cognitive assistant for the blind

description: To restore vision for the blind several prosthetic approaches have been
 explored that convey raw images to the brain. So far these schemes all
 suffer from a lack of bandwidth. An alternate approach would restore
 vision at the cognitive level, bypassing the need to convey sensory data.
 A wearable computer captures video and other data, extracts important
 scene knowledge, and conveys that to the user in compact form. Here we
 implement an intuitive user interface for such a device using augmented
 reality: each object in the environment has a voice and communicates with
 the user on command. With minimal training this system supports many
 aspects of visual cognition: obstacle avoidance, scene understanding,
 formation and recall of spatial memories, navigation. Blind subjects can
 traverse an unfamiliar multi-story building on their first attempt. To
 spur further development in this domain we developed an open-source
 environment for standardized benchmarking of visual assistive devices.
description: Source data and scripts
 for figure 1-5The compressed folder
 contains source data files and MATLAB scripts for generating plots from
 Figures 1-5.Source Data Figure
 1-5.rar
DOI: 10.5061/dryad.3rh2043
title: Data from: Landscape structure regulates pest control provided by ants in sun coffee farms

description: 1. Ants play a fundamental role in coffee pest control. Despite this,
 there is a lack of understanding about how landscape configuration and
 composition regulate the ecosystem service provided by ants in sun coffee
 farms within highly fragmented landscapes. 2. We measured whether
 landscape structure influences ants’ ability to regulate coffee berry
 borer (CBB) in sun coffee farms in Southeastern Brazil. Considering the
 ecological interactions between ants and CBB at three different stages of
 pest control (reduction of CBB presence, CBB infestation, and CBB bean
 damage), we measured pest control among 10 landscapes that represented a
 gradual difference in forest and coffee cover. We manipulated ants through
 exclusion experiments and tested whether interactions between ants and
 different landscape structure metrics (distance to forest fragments,
 2-km-level forest cover, and 300-m-level forest and coffee cover)
 influenced pest control. 3. The presence of ants reduced CBB presence and
 CBB damage by up to 40%. We show how pest control service indicators
 change depending on the landscape level. The probability of CBB presence
 increased with expanding coffee and forest cover at the 300-m-level but
 decreased at the 2-km-level. CBB infestation reduced further after 25m
 from forest edges, suggesting ants that provide these ecosystem services
 are adapted to matrix conditions in sun coffee farms. Ants reduced CBB
 presence, CBB infestation, and CBB damage in landscapes with at least 40%
 2-km-level forest cover. Beyond this threshold, there is a turning point
 for ecological processes involved in pest control. 4. Synthesis and
 applications. This is the first long-term branch-level exclusion
 experiment to present strong evidence of ants as efficient providers of
 pest control in sun coffee farms. We show how landscape structure
 modulates key ecological processes involved in three different ant-coffee
 berry borer (CBB) interactions that regulate CBB populations. Forest cover
 measured at different landscape levels yielded different results for CBB
 presence, emphasizing the importance of multi-scale studies for landscape
 management. Considering surrounding forest cover and crop proximity to
 forest fragments in planning the spatial arrangement of coffee farms can
 thus both improve pest control as well as contribute to biodiversity
 conservation.
description: CBB_damage_dryad_2_JAPPL_2017_01146.R2Data set with total number of coffee berries and damage inside bored berries. Used to test CBB damage, efficiency of the intensity of pest control service by ants.dryad_2_JAPPL_2017_01146.R2.xlsCBB_presence_infestation_dryad_JAPPL_2017_01146.R2Data set of the total number of coffee berries, number of bored berries, and ant activity. Used to test CBB presence and CBB infestation.dryad_JAPPL_2017_01146.R2.xls
DOI: 10.5061/dryad.2g7g3dc
title: Data from: Maladaptive shifts in life history in a changing environment

description: Many species facing climate change have complex life cycles, with
 individuals in different stages differing in their sensitivity to a
 changing climate and their contribution to population growth. We use a
 quantitative genetics model to predict the dynamics of adaptation in a
 stage-structured population confronted with a steadily changing
 environment. Our model assumes that different optimal phenotypic values
 maximize different fitness components, consistent with many empirical
 observations. In a constant environment, the population evolves towards an
 equilibrium phenotype, which represents the best compromise given the
 trade-off between vital rates. In a changing environment however, the mean
 phenotype in the population will lag behind this optimal compromise. We
 show that this lag may result in a shift along the trade-off between vital
 rates, with negative consequences for some fitness components, but, less
 intuitively, improvements in some others. Complex eco-evolutionary
 dynamics can emerge in our model due to feedbacks between population
 demography and adaptation. Because of such feedbacks loops, selection may
 favor further shifts in life history in the same direction as caused by
 maladaptive lags. These shifts in life history could be wrongly
 interpreted as adaptations to the new environment, while they only reflect
 the inability of the population to adapt fast enough.
description: Boechera-MaladaptationMathematica notebook for Boechera sp.Fagus-MaladaptationMathematica notebook for Fagus sp.
DOI: 10.5061/dryad.426658h
title: Data from: Assessing bottom-trawling impacts based on the longevity of benthic invertebrates

description: 1. Bottom trawling is the most widespread human activity directly
 affecting seabed habitats. Assessment and effective management of the
 effects of bottom trawling at the scale of fisheries requires an
 understanding of differences in sensitivity of biota to trawling.
 Responses to disturbance are expected to depend on the intrinsic rate of
 increase of populations (r), which is expected to be linearly related to
 the reciprocal of longevity. 2. We examine the relationship between the
 longevity of benthic invertebrates and their response to bottom trawling;
 both in terms of the immediate mortality following a trawl pass and their
 subsequent rates of recovery. We collate all available data from
 experimental and comparative trawling studies, and test how longevity
 influences these aspects of sensitivity. 3. The shortest-lived organisms
 (&lt;1yr) increased in abundance shortly after experimental trawling,
 but showed no response to trawling in longer-term comparative studies.
 Conversely, the abundance of biota with a life-span &gt;1yr decreased
 by ~9% immediately following a trawl pass. The effect of bottom trawling
 in comparative studies increased with longevity, with a 2-3× larger effect
 on biota living &gt;10yr than on biota living 1-3yr. We attribute this
 difference to the slower recovery rates of the longer-lived biota. 4. The
 observed relationship between the intrinsic rate of population increase
 (r, our metric of recovery rate) and the reciprocal of longevity matches
 theoretical expectation and predicts that the sensitivity of habitats to
 bottom trawling is higher in habitats with higher proportions of
 long-lived organisms. 5. Synthesis and Applications. Where the longevity
 of a species or the longevity distribution of a community is known or can
 be inferred, our estimates of depletion and intrinsic rate of increase can
 be combined with high-resolution maps of trawling intensity to assess
 trawling impacts at the scale of the fishery or other defined unit of
 assessment. Our estimates of r may also be used to estimate recovery times
 following other forms of seabed disturbance.06-Sep-2018
description: Fuzzy-coded
 longevityFuzzy-coded longevity
 for all taxa in the database, in four longevity classes (&lt;1, 1-3, 3-10,
 and &gt;10 years).Longevity.traits.csvComparative trawl studies dataData extracted in a systematic review of comparative bottom trawl studies The readme file gives a more detailed description of the headers.Comparative.data.csv