cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ck1rb1g
title: Data from: Age-specific offspring mortality economically tracks food abundance in a piscivorous seabird

description: Earlier offspring mortality prior to independence saves resources for kin,
 which should be more beneficial when food is short. Using 24 years of data
 on age-specific common tern (Sterna hirundo) chick mortality, best
 described by the Gompertz function, and estimates of energy consumption
 per age of mortality, we investigated how energy wasted on non-fledged
 chicks depends on brood size, hatching order and annual abundance of
 herring (Clupea harengus), the main food source. We found mortality
 directly after hatching (Gompertz baseline mortality) to be high and to
 increase with decreasing herring abundance. Mortality declined with age,
 at a rate relatively insensitive to herring abundance. The sensitivity of
 baseline mortality to herring abundance reduced energy wasted on
 non-fledged chicks when herring was short. Among chicks that did not
 fledge, last-hatched chicks were less costly than earlier hatched chicks,
 due to their earlier mortality. However, per hatchling produced, the least
 energy was wasted on chicks without siblings, due to their baseline
 mortality being most sensitive to herring abundance. We suggest that
 earlier mortality of offspring when food is short facilitates economic
 adjustment of post-hatching parental investment to food abundance, but
 that such economic brood reduction may be constrained by sibling
 competition.
description: Raw data age-specific
 chick survival and herring abundanceRaw data on age-specific
 survival (in days) of common tern chicks (hatched in a colony in
 Wilhelmshaven, Germany) in relation to year (1992-2015), brood size,
 hatching order and standardized North sea herring
 abundance.
DOI: 10.15468/dl.4rcqac
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aphthona abdominalis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 53 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000568-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1qj22
title: Data from: Preservation of potassium balance is strongly associated with insect cold tolerance in the field: a seasonal study of Drosophila subobscura

description: There is interest in pinpointing genes and physiological mechanisms
 explaining intra- and interspecific variations in cold tolerance, because
 thermal tolerance phenotypes strongly impact the distribution and
 abundance of wild animals. Laboratory studies have highlighted that the
 capacity to preserve water and ion homeostasis is linked to low
 temperature survival in insects. It remains unknown, however, whether
 adaptive seasonal acclimatization in free-ranging insects is governed by
 the same physiological mechanisms. Here, we test whether cold tolerance in
 field-caught Drosophila subobscura is high in early spring and lower
 during summer and whether this transition is associated with seasonal
 changes in the capacity of flies to preserve water and ion balance during
 cold stress. Indeed, flies caught during summer were less cold tolerant,
 and exposure of these flies to sub-zero temperatures caused a loss of
 haemolymph water and increased the concentration of K+ in the haemolymph
 (as in laboratory-reared insects). This pattern of ion and water balance
 disruption was not observed in more cold-tolerant flies caught in early
 spring. Thus, we here provide a field verification of hypotheses based on
 laboratory studies and conclude that the ability to maintain ion
 homeostasis is important for the ability of free-ranging insects to cope
 with chilling.
description: MacMillan et al Biol
 Lett - D.subobscura data archiveAn excel file containing
 all of the phenotypic and physiological data presented in the
 manuscript.MacMillan.etal.D.subobscura.data.archive.xlsx
DOI: 10.5061/dryad.nr607
title: Data from: It’s all in the timing: calibrating temporal penalties for biomedical data sharing

description: Objective: Biomedical science is driven by datasets that are being
 accumulated at an unprecedented rate, with ever-growing volume and
 richness. There are various initiatives to make these datasets more widely
 available to recipients who sign Data Use Certificate agreements, whereby
 penalties are levied for violations. A particularly popular penalty is the
 temporary revocation, often for several months, of the recipient’s data
 usage rights. This policy is based on the assumption that the value of
 biomedical research data depreciates significantly over time; however, no
 studies have been performed to substantiate this belief. This study
 investigates whether this assumption holds true and the data science
 policy implications. Methods: This study tests the hypothesis that the
 value of data for scientific investigators, in terms of the impact of the
 publications based on the data, decreases over time. The hypothesis is
 tested formally through a mixed linear effects model using approximately
 1200 publications between 2007 and 2013 that used datasets from the
 Database of Genotypes and Phenotypes, a data-sharing initiative of the
 National Institutes of Health. Results: The analysis shows that the impact
 factors for publications based on Database of Genotypes and Phenotypes
 datasets depreciate in a statistically significant manner. However, we
 further discover that the depreciation rate is slow, only ∼10% per year,
 on average. Conclusion: The enduring value of data for subsequent studies
 implies that revoking usage for short periods of time may not sufficiently
 deter those who would violate Data Use Certificate agreements and that
 alternative penalty mechanisms may need to be invoked.
description: Publication and dbGaP
 datasets mapping before triageThe dataset contains
 information derived from a corpus of 1205 publications, involving the
 analysis of dbGaP datasets, that were authored by approved recipients as
 of 2013. Each instance in the dataset corresponds to a publication, dbGaP
 dataset pair. Multiple instances are derived from a publication if it used
 more than one dbGaP dataset. This file contains the following information
 for each instance: the publication's pmid, pmcid, the dbGaP phs
 number, the journal title, the published date and the manuscript received
 date, the dbGaP dataset released date, the journal impact factor and
 eigenfactor score. A description of the columns in the dataset is
 available in the README file.publication_vs_dbgap_dataset_all_columns_before_triage.csvData used to fit the LME model after triageThis dataset contains the data that is used in the statistical analysis of the paper. This dataset is obtained from performing triage as described in the paper to the dataset with title "Publication and dbGaP datasets mapping before triage".publication_vs_dbgap_dataset_selected_columns_after_triage.csv
DOI: 10.5061/dryad.rq56t
title: Data from: Altered physical and social conditions produce rapidly reversible mating systems in water striders

description: Mating systems can vary within-species but the environmental drivers and
 behavioral mechanisms underlying this variation are seldom investigated
 experimentally. We experimentally assessed how individual behavioral
 plasticity in response to changes in pool and group size resulted in
 fundamental shifts in mating systems in water striders. We observed the
 same animals in larger and smaller pools, mimicking variation in pool size
 in natural streams, and observed a rapid, reversible change in the entire
 mating system. In large pools, striders exhibited scramble promiscuity
 with intense sexual conflict. Most males were active, harassing and
 driving females into hiding. Matings were frequent and typically lasted
 for more than 100 min. In contrast, when placed in small pools, the same
 animals often exhibited harem polygyny where the largest male drove other
 males into hiding, but allowed females to be relatively active. Matings
 were less frequent and of much shorter duration. Harem polygyny took
 several days to emerge after animals were moved to small pools, while
 these same animals returned to scramble promiscuity within hours after
 being moved to larger pools. Such variability in mating systems likely has
 important implications for the evolution of individual mating tactics.
description: data used in the
 manuscript and script to reproduce tables and figures.The zip file contains
 three data sets used in the study. data.striders.complete.sihetal.csv
 provides the activity and mating activity of individuals at each
 observation. data.striders.mating.durations.sihetal.csv provides the
 durations, individual identities, and other data associated with each
 mating observed. data.striders.mating.frequencies.sihetal.csv provides
 information on the number of mating of each individual each day. Each data
 set is also associated with a text meta-data file describing the meaning
 of the variables and the structure of the data. The zip file also contains
 the R script used to produce tables and figures in the manuscript. See the
 read me file for more information.data.striders.sihetal.zip
DOI: 10.5061/dryad.3v8c8j49
title: Data from: Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

description: Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous
 where they are sympatric, either naturally or due to introductions. The
 ability to detect hybridization between them has been hampered by a
 paucity of genetic markers that have been validated across the many
 phylogenetic lineages in the two species. Here, we describe 81 novel
 genetic markers and associated assays for discriminating the genomes of
 these sister species. These diagnostic nucleotide polymorphisms were
 discovered by sequencing of rainbow trout expressed sequence tags (ESTs)
 in a diverse panel of both cutthroat trout and steelhead/rainbow trout.
 The resulting markers were validated in a large number of lineages of both
 species, including all extant subspecies of cutthroat trout and most of
 the lineages of rainbow trout that are found in natural sympatry with
 cutthroat trout or used in stocking practices. Most of these markers (79%)
 distinguish genomic regions for all lineages of the two species, but a
 small number do not reliably diagnose coastal, westslope, and/or other
 subspecies of cutthroat trout. Surveys of natural populations and hatchery
 strains of trout and steelhead found rare occurrences of the alternative
 allele, which may be due to either previous introgression or shared
 polymorphism. The availability of a large number of genetic markers for
 distinguishing genomic regions originating in these sister species will
 allow the detection of both recent and more distant hybridization events,
 facilitate the study of the evolutionary dynamics of hybridization and
 provide a powerful set of tools for the conservation and management of
 both species.
description: Species_diagnostic_Suppl_tableSNP calls for all samples. C: homozygous O. clarki diagnostic; M: homozygous O. mykiss diagnostic; H: heterozygote; NC: no call; nr: assay not run or failed over entire Fluidigm plate.
DOI: 10.5061/dryad.5p51r
title: Data from: Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics

description: Symbioses include some of the clearest cases of coevolution, but their
 origin, loss, or reassembly with different partners can rarely be
 inferred. Here we use ant/plant symbioses involving three plant clades to
 investigate the evolution of symbioses. We generated phylogenies for the
 big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286
 species, as well as for five of their plant host groups, in each case
 sampling &gt;61% of the species. We show that the ant-housing
 Vachellia (Mimosoideae) clade and its ants co-diversified for the last 5
 Ma, with some species additionally colonized by younger plant-nesting ant
 species, some parasitic. An apparent co-radiation of ants and Tachigali
 (Caesalpinioideae) was followed by waves of colonization by the same ant
 clade, and subsequent occupation by a younger ant group. Wide crown and
 stem age differences between the ant-housing genus Triplaris
 (Polygonaceae) and its obligate ant inhabitants, and stochastic trait
 mapping, indicate that its domatium evolved earlier than the ants now
 occupying it, suggesting previous symbioses that dissolved. Parasitic ant
 species evolved from generalists, not from mutualists, and are younger
 than the mutualistic systems they parasitize. Our study illuminates the
 macroevolutionary assembly of ant/plant symbioses, which has been highly
 dynamic, even in very specialized systems.
description: Tachigali_matrix_chomicki_et_al_PRSBTachigali matrix containing 3 plastid markers (matK, trnL-trnF, psbA-trnH) and one nuclear (ITS)Vachellia_matrix_Chomicki_et_al_PRSB_dryadVachellia matrix containing three plastid markers (matK, trnL-trnF, psaB-rps14)Triplaris_Ruprechtia_matrix_Chomicki_et_al_PRSB_dryadTriplaris and Ruprechtia matrix with one nuclear (ITS) and four plastid markers (matK, ndhF, ndhC-trnV, rps16-trnK)Platymiscium_matrix_Chomicki_et_al_PRSB_dryadPlatymiscium matrix with one nuclear (ITS) and three plastid markers (matK, trnL intron, trnL-trnF spacer)
DOI: 10.5061/dryad.p4n0j
title: Data from: Decoupled post-glacial history in mutualistic plant-insect interactions: insights from the yellow loosestrife (Lysimachia vulgaris) and its associated oil-collecting bees (Macropis europaea and M. fulvipes)

description: Aim: We take a comparative phylogeographical approach to assess whether
 three species involved in a specialized oil-rewarding pollination system
 (i.e. Lysimachia vulgaris and two oil-collecting bees within the genus
 Macropis) show congruent phylogeographical trajectories during
 post-glacial colonization processes. Our working hypothesis is that within
 specialized mutualistic interactions, where each species relies on the
 co-occurrence of the other for survival and/or reproduction, partners are
 expected to show congruent evolutionary trajectories, because they are
 likely to have followed parallel migration routes and to have shared
 glacial refugia. Location: Western Palaearctic. Methods: Our analysis
 relies on the extensive sampling of 104 Western Palaearctic populations
 (totalling 434, 159 and 74 specimens of Lysimachia vulgaris, Macropis
 europaea and Macropis fulvipes, respectively), genotyped with amplified
 fragment length polymorphism. Based on this, we evaluated the regional
 genetic diversity (Shannon diversity and allele rarity index) and genetic
 structure (assessed using structure, population networks,
 isolation-by-distance and spatial autocorrelation metrics) of each
 species. Finally, we compared the general phylogeographical patterns
 obtained. Results: Contrary to our expectations, the analyses revealed
 phylogeographical signals suggesting that the investigated organisms
 demonstrate independent post-glacial trajectories as well as distinct
 contemporaneous demographic parameters, despite their mutualistic
 interaction. Main conclusions: The mutualistic partners investigated here
 are likely to be experiencing distinct and independent evolutionary
 dynamics because of their contrasting life-history traits (e.g. dispersal
 abilities), as well as distinct hubs and migration routes. Such conditions
 would prevent and/or erase any signature of co-structuring of lineages in
 space and time. As a result, the lack of phylogeographical congruence
 driven by differences in life-history traits might have arisen
 irrespective of the three species having shared similar Pleistocene
 glacial refugia.
description: Dryad_Triponezetal2014AFLP datasets. See Readme for details.
DOI: 10.15468/dl.qq5ube
title: Occurrence Download

description: A dataset containing 298 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Living Specimen, Specimen, Human Observation)",
 "Country is Türkiye",
 "TaxonKey is Cedrus libani"
 ]
}

 The dataset includes 298 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000569-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vh21c
title: Data from: Coalescent and biophysical models of stepping-stone gene flow in Neritid snails

description: Marine species in the Indo-Pacific have ranges that can span thousands of
 kilometers, yet studies increasingly suggest that mean larval dispersal
 distances are less than historically assumed. Gene flow across these
 ranges must therefore rely to some extent on larval dispersal among
 intermediate “stepping-stone” populations in combination with
 long-distance dispersal far beyond the mean of the dispersal kernel. We
 evaluate the strength of stepping-stone dynamics by employing a spatially
 explicit biophysical model of larval dispersal in the Tropical Pacific to
 construct hypotheses for dispersal pathways. We test these hypotheses with
 coalescent models of gene flow among high-island archipelagos in four
 Neritid gastropod species. Two of the species live in the marine
 intertidal, while the other two are amphidromous, living in freshwater but
 retaining pelagic dispersal. Dispersal pathways predicted by the
 biophysical model were strongly favored in 16 of 18 tests against
 alternate hypotheses. In regions where connectivity among high-island
 archipelagos was predicted as direct, there was no difference in gene flow
 between marine and amphidromous species. In regions where connectivity was
 predicted through stepping-stone atolls only accessible to marine species,
 gene flow estimates between high-island archipelagos were significantly
 higher in marine species. Moreover, one of the marine species showed a
 significant pattern of isolation-by-distance consistent with
 stepping-stone dynamics. While our results support stepping-stone dynamics
 in Indo-Pacific species, we also see evidence for non-equilibrium
 processes such as range expansions or rare long-distance dispersal events.
 This study provides an empirical assessment of a biophysical model that
 helps to shed light on larval dispersal pathways.
description: neritids_sample_localitiesPopulation serial numbers are given in samples names as ###.XX where ### is the serial number and XX is the number of the individual sample. Samples without serial numbers were kindly provided by Melissa Frey. Lat/Longs are probably not very accurate. - Eric Crandall July 6, 2012canalis-final-migrateInput file for Neritina canalis in Migrate format. Mitochondrial CO1 sequence collected with Folmer primers: HCO-2198, LCO-1490. See localities file for more information.dilatatum-final-migrateInput file for Neripteron dilatatum in Migrate format. Mitochondrial CO1 sequence collected with Folmer primers: HCO-2198, LCO-1490. See localities file for more information.plicata-final-migrateInput file for Nerita plicata in Migrate format. Mitochondrial CO1 sequence collected with Folmer primers: HCO-2198, LCO-1490. See localities file for more information.albicilla-final-migrateInput file for Nerita albicilla in Migrate format. Mitochondrial CO1 sequence collected with Folmer primers: HCO-2198, LCO-1490. See localities file for more information.
DOI: 10.5061/dryad.3mj3m
title: Data from: Mutations in global regulators lead to metabolic selection during adaptation to complex environments

description: Adaptation to ecologically complex environments can provide insights into
 the evolutionary dynamics and functional constraints encountered by
 organisms during natural selection. Adaptation to a new environment with
 abundant and varied resources can be difficult to achieve by small
 incremental changes if many mutations are required to achieve even modest
 gains in fitness. Since changing complex environments are quite common in
 nature, we investigated how such an epistatic bottleneck can be avoided to
 allow rapid adaptation. We show that adaptive mutations arise repeatedly
 in independently evolved populations in the context of greatly increased
 genetic and phenotypic diversity. We go on to show that weak selection
 requiring substantial metabolic reprogramming can be readily achieved by
 mutations in the global response regulator arcA and the stress response
 regulator rpoS. We identified 46 unique single-nucleotide variants of arcA
 and 18 mutations in rpoS, nine of which resulted in stop codons or large
 deletions, suggesting that subtle modulations of ArcA function and
 knockouts of rpoS are largely responsible for the metabolic shifts leading
 to adaptation. These mutations allow a higher order metabolic selection
 that eliminates epistatic bottlenecks, which could occur when many changes
 would be required. Proteomic and carbohydrate analysis of adapting E. coli
 populations revealed an up-regulation of enzymes associated with the TCA
 cycle and amino acid metabolism, and an increase in the secretion of
 putrescine. The overall effect of adaptation across populations is to
 redirect and efficiently utilize uptake and catabolism of abundant amino
 acids. Concomitantly, there is a pronounced spread of more ecologically
 limited strains that results from specialization through metabolic
 erosion. Remarkably, the global regulators arcA and rpoS can provide a
 “one-step” mechanism of adaptation to a novel environment, which
 highlights the importance of global resource management as a powerful
 strategy to adaptation.
description: Saxer_et_al_PlosGen_CarbohydrateDataData from carbohydrate analyses of cell extract and spend media from E. coli RU1 ancestor and E. coli RU1-BHI evolved populationsSaxer_et_al_PlosGen_pHpH of stationary phase cultures of the ancestor and evolved populations of E. coli RU1 and C. freundii RU2 in LB and BHI (in their selective media)Saxer_et_al_PlosGen_MigrationDataMigration data of single colonies isolated from the populations of E. coli and C. freundii evolved in LB and BHISaxer_et_al_PlosGen_GrowthOD600_BHIOD readings of E. coli and C. freundii populations evolved in BHI over the course of a growth cycle in BHISaxer_et_al_PlosGen_GrowthOD600_LBOD readings of LB-evolved populations of E. coli and C. freundii in LB with the respective ancestorsSaxer_et_al_PlosGen_PopulationKey_correctedThis files contains the name of all the populations and ancestors, their selection regime and the accession number for the genomic and proteomics data, if applicable.