cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.037jr6v
title: Data from: Catastrophic dynamics limit Atlantic cod recovery

description: Collapses and regime changes are pervasive in complex systems (such as
 marine ecosystems) governed by multiple stressors. The demise of Atlantic
 cod (Gadus morhua) stocks constitutes a text book example of the
 consequences of overexploiting marine living resources, yet the drivers of
 these nearly synchronous collapses are still debated. Moreover, it is
 still unclear why rebuilding of collapsed fish stocks such as cod is often
 slow or absent. Here we apply the stochastic cusp model, based on
 catastrophe theory, and show that collapse and recovery of cod stocks are
 potentially driven by the specific interaction between exploitation
 pressure and environmental drivers. Our statistical modelling study
 demonstrates that for most of the cod stocks ocean warming could induce a
 non-linear discontinuous relationship between fishing pressure and stock
 size, which would explain hysteresis in their response to reduced
 exploitation pressure. Our study suggests further that a continuing
 increase in ocean temperatures will likely limit productivity and hence
 future fishing opportunities for most cod stocks of the Atlantic Ocean.
 Moreover, our study contributes to the ongoing discussion on the
 importance of climate and fishing effects on commercially exploited fish
 stocks, highlighting the importance of considering discontinuous dynamics
 in holistic ecosystem-based management approaches, particularly under
 climate change.
description: Data of Atlantic cod
 stockHere the data of
 Spawning Stock Biomass (SSB), Fishing Mortality (F) and Sea Surface
 Temperature (SST) for the 19 cod stocks used in the study can be found.
 SSB and F derived from stock assessment developed by the institutions
 across the North Atlantic: International Council for the Exploration of
 the Sea (ICES), Northwest Atlantic Fisheries Organization (NAFO),
 Fisheries and Oceans Canada also known as Department of Fisheries and
 Oceans (DFO), and National Oceanic and Atmospheric Administration (NOAA).
 The SST were collated from the NOAA Extended Reconstructed Sea Surface
 Temperature dataset (ERSST, www.ncdc.noaa.gov) version 4. Accessed in July
 of 2017. If you use these SST data, please cite the original data source:
 Boyin Huang, Viva F. Banzon, Eric Freeman, Jay Lawrimore, Wei Liu, Thomas
 C. Peterson, Thomas M. Smith, Peter W. Thorne, Scott D. Woodruff, and
 Huai-Min Zhang, 2015: Extended Reconstructed Sea Surface Temperature
 (ERSST), Version 4. Sea Surface Temperature. NOAA National Centers for
 Environmental Information. doi:10.7289/V5KD1VVF [accessed July
 2017].data_Sguotti_et_al.xlsx
DOI: 10.15468/dl.bubjbj
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coeloneurum ferrugineum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 49 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000877-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.42g78nj
title: Data from: Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species

description: Background: Plukenetia is a small pantropical genus of lianas and vines
 with variably sized edible oil-rich seeds that presents an ideal system to
 investigate neotropical and pantropical diversification patterns and seed
 size evolution. We assessed the biogeography and seed evolution of
 Plukenetia through phylogenetic analyses of a 5,069 character molecular
 dataset comprising five nuclear and two plastid markers for 86 terminals
 in subtribe Plukenetiinae (representing 20 of ~23 Plukenetia species). Two
 nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for
 the first time. Our goals were: (1) produce a robust, time-dependent
 evolutionary framework for Plukenetia using BEAST; (2) reconstruct its
 biogeographical history with ancestral range estimation in BioGeoBEARS;
 (3) define seed size categories; (4) identify patterns of seed size
 evolution using ancestral state estimation; and (5) conduct regression
 analyses with putative drivers of seed size using the threshold model.
 Results: Plukenetia was resolved into two major groups, which we refer to
 as the pinnately- and palmately-veined clades. Our analyses suggest
 Plukenetia originated in the Amazon or Atlantic Forest of Brazil during
 the Oligocene (28.7 Mya) and migrated/dispersed between those regions and
 Central America/Mexico throughout the Miocene. Trans-oceanic dispersals
 explain the pantropical distribution of Plukenetia, including from the
 Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to
 Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and
 Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds
 in the ancestor of Plukenetia. Seed size fits a Brownian motion model of
 trait evolution and is moderately to strongly associated with plant size,
 fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not
 drivers of seed size, although there was a weak association with a
 transition to fire prone semi-arid savannas. Conclusions: The major
 relationships among the species of Plukenetia are now well-resolved. Our
 biogeographical analyses support growing evidence that many pantropical
 distributions developed by periodic trans-oceanic dispersals throughout
 the Miocene and Pliocene. Selection on a combination of traits contributed
 to seed size variation, while movement between forest edge/light gap and
 canopy niches likely contributed to the seed size extremes in Plukenetia.
description: Cardinal-McTeague_2018This package includes the LiteBlueDevil v0.3 python script, archived alignment, tree files, and seed dimension dataset, and R script and files needed to reproduce the seed evolution analyses in the following paper: Cardinal-McTeague et al. 2018. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evolutionary Biology.
DOI: 10.5061/dryad.5b5d0
title: Data from: Timing of breeding in an ecologically trapped bird

description: In human-modified environments, organisms may prefer to use habitats where
 their reproductive performance is lower compared to alternative options.
 Many such ecological traps occur in seasonally changing environments.
 Although the timing of breeding has been shown to impact reproductive
 performance in a variety of organisms, it has never been considered as a
 potential mechanism underlying ecological traps. We address this issue
 with a migratory bird, the Red-backed shrike, breeding in a
 human-modified, farmland-forest landscape. Shrikes prefer breeding in
 forest clear-cuts where their reproductive performance is lower than in
 less attractive farmland. We compared brood size and quality of early
 (first broods) and delayed breeders (replacement broods) between the two
 habitats. We found a stronger seasonal decrease in reproductive
 performance in preferred forest clear-cuts than in farmland. Food
 resources were slightly more abundant in forest than in farmland at the
 beginning of the season but depleted more steeply in forest by the end of
 the breeding season. By contrast, the phenotypic quality of breeders did
 not decline over the course of the season in either habitat. This is the
 first report that the timing of breeding relative to the seasonal change
 in key resources may play a significant role in explaining low
 reproductive performance in ecological traps.
description: Data 'Timing of
 breeding in an ecologically trapped bird'Data in different sheets
 depending on the analyses presented in Materials &
 MethodsData_Hollander et al. (2017)
 Am. Nat..xlsx
DOI: 10.5061/dryad.28jn6
title: Data from: Decreased brain levels of vitamin B12 in aging, autism and schizophrenia

description: Many studies indicate a crucial role for the vitamin B12 and
 folate-dependent enzyme methionine synthase (MS) in brain development and
 function, but vitamin B12 status in the brain across the lifespan has not
 been previously investigated. Vitamin B12 (cobalamin, Cbl) exists in
 multiple forms, including methylcobalamin (MeCbl) and adenosylcobalamin
 (AdoCbl), serving as cofactors for MS and methylmalonylCoA mutase,
 respectively. We measured levels of five Cbl species in postmortem human
 frontal cortex of 43 control subjects, from 19 weeks of fetal development
 through 80 years of age, and 12 autistic and 9 schizophrenic subjects.
 Total Cbl was significantly lower in older control subjects (&gt; 60
 yrs of age), primarily reflecting a &gt;10-fold age-dependent decline
 in the level of MeCbl. Levels of inactive cyanocobalamin (CNCbl) were
 remarkably higher in fetal brain samples. In both autistic and
 schizophrenic subjects MeCbl and AdoCbl levels were more than 3-fold lower
 than age-matched controls. In autistic subjects lower MeCbl was associated
 with decreased MS activity and elevated levels of its substrate
 homocysteine (HCY). Low levels of the antioxidant glutathione (GSH) have
 been linked to both autism and schizophrenia, and both total Cbl and MeCbl
 levels were decreased in glutamate-cysteine ligase modulatory subunit
 knockout (GCLM-KO) mice, which exhibit low GSH levels. Thus our findings
 reveal a previously unrecognized decrease in brain vitamin B12 status
 across the lifespan that may reflect an adaptation to increasing
 antioxidant demand, while accelerated deficits due to GSH deficiency may
 contribute to neurodevelopmental and neuropsychiatric disorders.
description: Zhang et al. Plos One
 manuscript dataCobalamin and thiol
 metabolite data are provided for the specified Figures.
DOI: 10.5061/dryad.sp01m
title: Data from: Effects of interference between selected loci on the mutation load, inbreeding depression and heterosis

description: A classical prediction from single-locus models is that inbreeding
 increases the efficiency of selection against partially recessive
 deleterious alleles (purging), thereby decreasing the mutation load and
 level of inbreeding depression. However, previous multilocus simulation
 studies found that increasing the rate of self-fertilization of
 individuals may not lead to purging and argued that selective interference
 among loci causes this effect. In this article, I derive simple analytical
 approximations for the mutation load and inbreeding depression, taking
 into account the effects of interference between pairs of loci. I consider
 two classical scenarios of nonrandomly mating populations: a single
 population undergoing partial selfing and a subdivided population with
 limited dispersal. In the first case, correlations in homozygosity between
 loci tend to reduce mean fitness and increase inbreeding depression. These
 effects are stronger when deleterious alleles are more recessive, but only
 weakly depend on the strength of selection against deleterious alleles and
 on recombination rates. In subdivided populations, interference increases
 inbreeding depression within demes, but decreases heterosis between demes.
 Comparisons with multilocus, individual-based simulations show that these
 analytical approximations are accurate as long as the effects of
 interference stay moderate, but fail for high deleterious mutation rates
 and low dominance coefficients of deleterious alleles.
description: C++ simulation program,
 partially selfing populationselfing.tarC++ simulation program, partial selfing, distribution of mutational effectsselfingDistr.tarC++ simulation program, island modelisland.tar
DOI: 10.5061/dryad.1fc41
title: Data from: Social selection parapatry in Afrotropical sunbirds

description: The extent of range overlap of incipient and recent species depends on the
 type and magnitude of phenotypic divergence that separates them, and the
 consequences of phenotypic divergence on their interactions. Signal
 divergence by social selection likely initiates many speciation events,
 but may yield niche-conserved lineages predisposed to limit each others’
 ranges via ecological competition. Here we examine this neglected aspect
 of social selection speciation theory in relation to the discovery of a
 non-ecotonal species border between sunbirds. We find that Nectarinia
 moreaui and N. fuelleborni meet in a ∼6 km wide contact zone, as estimated
 by molecular cline analysis. These species exploit similar bioclimatic
 niches, but sing highly divergent learned songs, consistent with
 divergence by social selection. Cline analyses suggest that within-species
 stabilizing social selection on song-learning predispositions maintains
 species differences in song despite both hybridization and cultural
 transmission. We conclude that ecological competition between moreaui and
 fuelleborni contributes to the stabilization of the species border, but
 that ecological competition acts in conjunction with reproductive
 interference. The evolutionary maintenance of learned song differences in
 a hybrid zone recommend this study system for future studies on the
 mechanisms of learned song divergence and its role in speciation.
description: sunbird_data_fordryadThe data file contains two worksheets with data on Nectarinia moreaui and N. fuelleborni, one with data from sonogram-based measurements of song recordings, and one with measurements of culmen and upper mandible length.
DOI: 10.5061/dryad.101tb
title: Data from: Recurrent evolution of dioecy in bryophytes

description: The origin and maintenance of separate sexes (dioecy) is an enduring
 evolutionary puzzle. Although both hermaphroditism and dioecy occur in
 many diverse clades, we know little about the long-term evolutionary
 consequences of changing sexual system. Here we find evidence for at least
 133 transitions between sexual systems in mosses, representing an almost
 unparalleled lability in the evolution of their sexual systems.
 Furthermore, in contrast to predictions, the transition rate from
 hermaphroditism to dioecy was approximately twice as high as the reverse
 transition. Our results also suggest that hermaphodites may have higher
 rates of diversification than dioecious mosses. These results illustrate
 the utility of mosses for understanding the genomic and macroevolutionary
 consequences of hermaphroditism and dioecy.
description: Recurrent evolution of
 dioecy in bryophytesThis file includes
 species of mosses used in the phylogenetic analysis of Shaw et al. 2005
 Taxon; the sexuality of each species (dioicous = separate gametophyte
 sexes; autoicious = hermaphroditic; for a description of moss sexuality
 terms, see http://en.wikipedia.org/wiki/Dioicous); the sexuality of each
 genus; and the number of recognized species in each
 genus.
DOI: 10.5061/dryad.0jd3t
title: Data from: Limb-bone loading in swimming turtles: changes in loading facilitate transitions from tubular to flipper-shaped limbs during aquatic invasions

description: Members of several terrestrial vertebrate lineages have returned to nearly
 exclusive use of aquatic habitats. These transitions were often
 accompanied by changes in skeletal morphology, such as flattening of limb
 bone shafts. Such morphological changes might be correlated with the
 exposure of limb bones to altered loading. Though the environmental forces
 acting on the skeleton differ substantially between water and land, no
 empirical data exist to quantify the impact of such differences on the
 skeleton, either in terms of load magnitude or regime. To test how
 locomotor loads change between water and land, we compared in vivo strains
 from femora of turtles (Trachemys scripta) during swimming and terrestrial
 walking. As expected, strain magnitudes were much lower (by 67.9%) during
 swimming than during walking. However, the loading regime of the femur
 also changed between environments: torsional strains are high during
 walking, but torsion is largely eliminated during swimming. Changes in
 loading regime between environments may have enabled evolutionary shifts
 to hydrodynamically advantageous flattened limb bones in highly aquatic
 species. Although circular cross sections are optimal for resisting
 torsional loads, the removal of torsion would reduce the advantage of
 tubular shapes, facilitating the evolution of flattened limbs.
description: Young&Blob_TurtleFemurStrainData_DryadPeak strain data from turtle femoral mid-shafts during swimming and terrestrial walking.
DOI: 10.5061/dryad.5q400
title: Data from: Historically browsed jewelweed populations exhibit greater tolerance to deer herbivory than historically protected populations

description: Browsing by overabundant white-tailed deer (Odocoileus virginianus) has
 altered ecological relationships in forest communities across eastern
 North America. Recent but limited work suggests that deer browsing also
 selects for particular plant defensive traits. We hypothesized that
 browsing by deer has imposed selection on defensive traits in an annual
 native wildflower, orange jewelweed (Impatiens capensis). To test this
 hypothesis, we collected individuals from 26 natural populations across a
 5000 km2 area in New York State, USA. Half of these populations were
 historically protected from deer and half were exposed to heavy browsing.
 We planted individuals in common gardens subjected to natural deer
 browsing or no browsing. Individuals from historically browsed populations
 exhibited significantly higher tolerance than those from historically
 protected populations. Herbivory by deer reduced lifetime fruit production
 by only 20% in historically browsed populations, as opposed to 57% in
 historically protected populations. Two mechanisms were correlated with
 this increased tolerance: increased number of flowering days and increased
 fruits per flowering node. Synthesis The increased tolerance of
 historically browsed populations suggests that these populations evolved
 increased tolerance or that historically protected populations lost
 tolerance over time. Variation in tolerance traits in native plant species
 may allow them to persist in the face of rapid ecological change.
description: Data from Martin et al.
 2014 Journal of EcologyData from: Historically
 browsed jewelweed populations exhibit greater tolerance to deer herbivory
 than historically protected populations, Martin, Laura, Agrawal, Anurag,
 Kraft, CliffordMartin et al
 2014.xlsx
DOI: 10.5061/dryad.p52qh
title: Data from: Management of pulmonary nodules by community pulmonologists

description: BACKGROUND: Pulmonary nodules (PNs) are a common reason for referral to
 pulmonologists. The majority of data for the evaluation and management of
 PNs is derived from studies performed in academic medical centers. Little
 is known about the prevalence and diagnosis of PNs, the use of diagnostic
 testing, or the management of PNs by community pulmonologists. METHODS:
 This multicenter observational record review evaluated 377 patients aged
 40 to 89 years referred to 18 geographically diverse community pulmonary
 practices for intermediate PNs (8-20 mm). Study measures included the
 prevalence of malignancy, procedure/test use, and nodule pretest
 probability of malignancy as calculated by two previously validated
 models. The relationship between calculated pretest probability and
 management decisions was evaluated. RESULTS: The prevalence of malignancy
 was 25% (n = 94). Nearly one-half of the patients (46%, n = 175) had
 surveillance alone. Biopsy was performed on 125 patients (33.2%). A total
 of 77 patients (20.4%) underwent surgery, of whom 35% (n = 27) had benign
 disease. PET scan was used in 141 patients (37%). The false-positive rate
 for PET scan was 39% (95% CI, 27.1%-52.1%). Pretest probability of
 malignancy calculations showed that 9.5% (n = 36) were at a low risk,
 79.6% (n = 300) were at a moderate risk, and 10.8% (n = 41) were at a high
 risk of malignancy. The rate of surgical resection was similar among the
 three groups (17%, 21%, 17%, respectively; P = .69). CONCLUSIONS: A
 substantial fraction of intermediate-sized nodules referred to
 pulmonologists ultimately prove to be lung cancer. Despite advances in
 imaging and nonsurgical biopsy techniques, invasive sampling of low-risk
 nodules and surgical resection of benign nodules remain common, suggesting
 a lack of adherence to guidelines for the management of PNs.
description: Data supporting
 publicationThis is the source data
 for the publication.chart_review_v1.xlsx
DOI: 10.5061/dryad.8261b
title: Data from: Evolution on the move: specialization on widespread resources associated with rapid range expansion in response to climate change

description: Generalist species and phenotypes are expected to perform best under rapid
 environmental change. In contrast to this view that generalists will
 inherit the Earth, we find that increased specialisation on a single host
 plant is associated with the recent climate-driven range expansion of the
 UK Brown Argus butterfly. Field assays of female host plant preference
 across the UK reveal a diversity of adaptations to host plants in
 long-established parts of the range, whereas butterflies in
 recently-colonized areas are more specialised, consistently preferring to
 lay eggs on one host plant species that is geographically widespread
 throughout the region of expansion, despite being locally rare. By
 common-garden rearing of females’ offspring we also show an increase in
 dispersal propensity associated with the colonization of new sites. Range
 expansion is therefore associated with an increase in the spatial scale of
 adaptation as dispersive specialists selectively spread into new regions.
 Major restructuring of patterns of local adaptation is likely to occur
 across many taxa with climate change, as lineages suited to regional
 colonization rather than local success emerge and expand.
description: Counts of eggs laid on
 experimental host plants placed at field sitesBA_hostpref_host.tetrads.txtSurvival data for brown argus butterfly laboratory rearing studySurvival.txtFlight morphology data for female brown argus butterflies reared in laboratory conditionsIndividual data_females.morphology.txtFlight morphology data for male brown argus butterflies reared in laboratoryIndividual data_males.morphology.txt