cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mgqnk98wn
title: Data from: Ovipositor and mouthparts in a fossil insect support a novel ecological role for early orthopterans in 300 million years old forests

description: A high portion of the earliest known, Pennsylvanian, insect fauna is
 composed of the so-called ‘lobeattid insects’, which systematic affinities
 and role as foliage feeders remain debated. We investigated hundreds of
 samples of a new lobeattid species from the Xiaheyan locality using a
 combination of photographic techniques, including Reflectance Transforming
 Imaging, and geometric morphometrics, to document its morphology, and
 infer its phylogenetic position and ecological role. Ctenoptilus frequens
 sp. nov. possessed a sword-shaped ovipositor whose valves interlocked by
 two ball-and-socket mechanisms. This unambiguously supports lobeattids as
 stem-relatives of all living Orthoptera (crickets, grasshoppers,
 katydids). Given the herein presented and other remains, it follows that
 this group experienced an early diversification coupled with high numbers
 of individuals. The ovipositor shape additionally indicates that ground
 was the preferred substrate for eggs. Visible mouthparts made it possible
 to assess the efficiency of the mandibular food uptake system in
 comparison to a wide array of extant species. The new species was
 omnivorous which explains the paucity of external damage on
 contemporaneous plant foliage.
description: Thank you for your interest in this dataset. It contains 36 .zip
 folders, 13 RTI files, and two animated .gif files.
 Each .zip folder contains a set of original photographs of a
 given specimen, or specimen area, of <i>Ctenoptilus
 frequens</i>. Each folder name indicates (i) the corresponding
 specimen number (e.g. ‘CNU-NX1-326’) complemented by (ii) indication on
 the corresponding morphological area (e.g. ‘habitus’, ‘head’). Each folder
 contains original .tif files, which name includes an indication on the
 photographed specimen imprint (‘p’ for ‘part’ and ‘c’ for ‘counterpart’;
 or ‘a’ and ‘b’), when applicable, and whether the specimen was
 photographed under dry condition (‘dry’) or under a thin film of ethanol
 (‘eth’). If not visible on photographs, a separate .tif file provides a
 scale (in millimetres). Each folder also contains an Adode Photoshop file
 with the complete set of aligned photographs, each composing a distinct
 layer, optimized. In a similar fashion, the file name
 of RTI files indicates (i) the specimen number (e.g. ‘CNU-NX1-326’)
 complemented by (ii) indication on the corresponding imprint (e.g. ‘c’,
 ‘p’) and (iii) indication on the corresponding area (e.g.
 ‘head’). The .gif file named
 phylomorphospace3d_diet_labels is an animated version
 of Fig. 3E with color-coding applying to diet (<i>Ctenoptilus
 frequens</i> in black) The .gif file named
 phylomorphospace3d_order_labels is an animated version
 of Fig. 3E with color-coding applying to orders (<i>Ctenoptilus
 frequens</i> in black).
DOI: 10.5061/dryad.6q573n5w2
title: The tepary bean genome provides insight into evolution and domestication under heat stress

description: Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert,
 is highly adapted to heat and drought. It is a sister species of common
 bean (Phaseolus vulgaris L.), the most important legume protein source for
 direct human consumption, and whose production is threatened by climate
 change. Analysis of the tepary genome revealed mechanisms for resilience
 to moderate heat stress and a reduced disease resistance gene repertoire,
 consistent with adaptation to arid, hot environments. Extensive
 collinearity and shared gene content among these Phaseolus species will
 facilitate engineering climate adaptation in common bean, a key food
 security crop, and accelerate tepary bean improvement.
DOI: 10.5061/dryad.cfxpnvx2v
title: Data from: No‐till establishment improves the climate benefit of bioenergy crops on marginal grasslands

description: Expanding biofuel production is expected to accelerate the conversion of
 unmanaged marginal lands to meet biomass feedstock needs. Greenhouse gas
 production during conversion jeopardizes ensuing climate benefits, but
 most research to date has focused only on conversion to annual crops and
 only following tillage. Here we report the global warming impact of
 converting USDA Conservation Reserve Program (CRP) grasslands to three
 types of bioenergy crops using no-till (NT) versus conventional tillage
 (CT). In three CRP fields planted to continuous corn, switchgrass, or
 restored prairie we established replicated NT and CT plots. For the two
 years following an initial soybean year in all fields, we found that, on
 average, NT conversion reduced nitrous oxide (N2O) emissions by 50% and
 carbon dioxide (CO2) emissions by 20% compared to CT conversion.
 Differences were higher in year 1 than in year 2 in the continuous corn
 field, and in the two perennial systems the differences disappeared after
 year 1. In all fields net CO2 emissions (as measured by eddy covariance)
 were positive for the first two years following CT establishment, but
 following NT establishment net CO2 emissions were close to zero or
 negative, indicating net C sequestration. Overall, NT improved the global
 warming impact of biofuel crop establishment following CRP conversion by
 over 20-fold compared to CT (-6.01 Mg CO2e ha-1 yr-1 for NT vs. -0.25 Mg
 CO2e ha-1 yr-1 for CT, on average). We also found that IPCC estimates of
 N2O emissions (as measured by static chambers) greatly underestimated
 actual emissions for converted fields regardless of tillage. Policies
 should encourage adoption of NT for converting marginal grasslands to
 perennial bioenergy crops in order to reduce carbon debt and maximize
 climate benefits.
description: Methods of data collection and processing are given in the
 associated SSSAJ publication.
description: Data set description is given in the file
 "readme_no-till_establishment.txt".
DOI: 10.15468/dl.gqfrt2
title: Occurrence Download

description: A dataset containing 52822 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Chordata [GBIF Backbone Taxonomy], Plantae [GBIF Backbone Taxonomy])",
 "GadmGid is one of (COL.15.27_2)"
 ]
 }
 ]
}

 The dataset includes 52822 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002243-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gm3
title: Benthos Dataset; segmented photomosaics from three oceanic environments

description: Reefs constitute some of the richest and most diverse
 environments on the planet, manifesting in complex biogenic 3D
 structures. As such, they are intensively studied. In benthic
 images, full segmentation (where every pixel is classified) is
 difficult and labour-intensive to achieve using human-based
 manual labeling. To solve that, we utilize label-augmentation,
 i.e., propagation of sparse manual labels to accelerate this task
 and achieve full map segmentation. The Benthos dataset contains
 fully labeled photomosaics from three oceanic environments with over 4500
 segmented objects useful for research in computer-vision and benthic
 ecology. This folder also contains a Matlab script for extracting
 community statistics from labeled photomosaics.
DOI: 10.5061/dryad.8sf7m0cj9
title: Experimental modification of morphology reveals the effects of the zygosphene-zygantrum joint on the range of motion of snake vertebrae

description: Variation in joint shape and soft tissue can alter range of motion (ROM)
 and create trade-offs between stability and flexibility. The shape of the
 distinctive zygosphene–zygantrum joint of snake vertebrae has been
 hypothesized to prevent axial torsion (twisting), but its function has
 never been tested experimentally. We used experimental manipulation of
 morphology to determine the role of the zygosphene–zygantrum articulation
 by micro-computed tomography (μCT) scanning and 3D printing two mid-body
 vertebrae with unaltered shape and with the zygosphene digitally removed
 for four species of phylogenetically diverse snakes. We recorded the
 angular ROM while manipulating the models in yaw (lateral bending), pitch
 (dorsoventral bending) and roll (axial torsion). Removing the zygosphene
 typically increased yaw and dorsal pitch ROM. In the normal vertebrae,
 roll was &lt;2.5 deg for all combinations of pitch and yaw. Roll
 increased in altered vertebrae but only for combinations of high yaw and
 ventral pitch that were near or beyond the limits of normal vertebra ROM.
 In the prairie rattlesnake and brown tree snake, roll in the altered
 vertebrae was always limited by bony processes other than the zygosphene,
 whereas in the altered vertebrae of the corn snake and boa constrictor,
 roll ROM was unconstrained when the pre- and post-zygapophyses no longer
 overlapped. The zygosphene acts as a bony limit for yaw and dorsal pitch,
 indirectly preventing roll by precluding most pitch and yaw combinations
 where roll could occur and potentially allowing greater forces to be
 applied across the vertebral column than would be possible with only
 soft-tissue constraints.
description: This dataset of multiple snake vertebrae was collected using a
 Skyscan Micro-CT 1172 scanner, segmented using Adobe Photoshop and FIJI,
 and finally manipulated and rendered using a combination of FIJI, MeshLab,
 and Meshmixer.
DOI: 10.5061/dryad.np5hqbzq0
title: Hybridization and transgressive exploration of colour pattern and wing morphology in Heliconius butterflies

description: Hybridization can generate novel phenotypes distinct from those of
 parental lineages, a phenomenon known as transgressive trait variation.
 Transgressive phenotypes might negatively or positively affect hybrid
 fitness, and increase available variation. Closely related species of
 Heliconius butterflies regularly produce hybrids in nature and
 hybridization is thought to play a role in the diversification of novel
 wing colour patterns despite strong stabilizing selection due to
 interspecific mimicry. Here, we studied wing phenotypes in first and
 second generation hybrids produced by controlled crosses between either
 two co-mimetic species of Heliconius or between two non-mimetic species.
 We quantified wing size, shape and colour pattern variation and asked
 whether hybrids displayed transgressive wing phenotypes. Discrete traits
 underlain by major-effect loci, such as the presence or absence of colour
 patches, generate novel phenotypes. For quantitative traits, such as wing
 shape or subtle colour pattern characters, hybrids only exceed the
 parental range in specific dimensions of the morphological space. Overall,
 our study addresses some of the challenges in defining and measuring
 phenotypic transgression for multivariate traits and our data suggest that
 the extent to which transgressive trait variation in hybrids contributes
 to phenotypic diversity depends on the complexity and the genetic
 architecture of the traits.
description: The data deposited here are the raw quantification of wing shape
 and pattern of Heliconius butterflies resulting from controlled
 inter-specific crosses and individuals from the parental species. They
 were obtained by analysing wing pictures through an analysis of pattern
 with a method called CPM (Le Poul et al, 2014) and geometric
 morphometry.
description: In the pattern tab, each column is a principal component of an
 analysis of pattern taking into account the colour of each
 pixel. In the shape tab, each column is the coordinate
 of the landmarks (20 for the forewing, FW, 18 for the hindwing,
 HW) In all tabs, 4 columns include the id of the
 specimen, its sex, origin and species status (Panama: CP = H. cydno
 chioneus, MP = H. melpomene rosina, MPxCP = F1 hybrid between H. cydno
 chioneus and H. melpomene rosina, CPx(MPxCP)= backcross towards H. cydno
 chioneus, MPx(MPxCP)= backcross towards H. melpomene rosina  --- Peru: T=
 H. timareta thelxinoe, M, H. melpomene amaryllis, F1= F1 hybrid between H.
 timareta thelxinoe and .H melpomene amaryllis, BT= backcross towards H.
 timareta thelxinoe, BM= backcross towards H. melpomene
 amaryllis) Original pictures and scripts used to
 analyse the datasets can be provided by the 1st author (CM) upon
 request.
DOI: 10.5061/dryad.qbzkh18dt
title: Orthostatic hypotension, dizziness, neurology outcomes, and death in older adults, supplement methods & tables, STROND checklist

description: Objective To test the hypothesis that orthostatic hypotension (OH) might
 cause cerebral hypoperfusion and injury, we examined the longitudinal
 relationship between orthostatic hypotension (OH) or orthostatic symptoms
 and incident neurologic outcomes in a community population of older
 adults. Methods Cardiovascular Health Study (CHS) participants (≥65yrs)
 without dementia or stroke had blood pressure (BP) measured after lying
 20-minutes and after standing 3-minutes. Participants reported dizziness
 immediately upon standing and any dizziness in the past 2wks. OH was
 defined as a drop in standing systolic/diastolic BP ≥20/≥10mmHg. We
 determined the association between OH or dizziness with (1) MRI brain
 findings (ventricular size, white matter hyperintensities, brain infarcts)
 using linear or logistic regression, (2) cognitive function (baseline and
 over time) using generalized estimating equations, and (3) prospective
 adjudicated events (dementia, stroke, death) using Cox models. Models were
 adjusted for demographic characteristics and OH risk factors. We used
 multiple imputation to account for missing OH or dizziness (N=534).
 Results Prior to imputation, there were 5,007 participants (mean age
 72.7±5.5yrs, 57.6% women, 10.9% black, 16% with OH). OH was modestly
 associated with death (HR=1.11; 95%CI:1.02,1.20), but not MRI findings,
 cognition, dementia, or stroke. In contrast, dizziness upon standing was
 associated with lower baseline cognition (β=-1.20;-1.94,-0.47), incident
 dementia (HR=1.32;1.04,1.62), incident stroke (HR=1.22;1.06,1.41), and
 death (HR=1.13; 1.06,1.21). Similarly, dizziness over the past two weeks
 was associated with higher white matter grade (β=0.16;0.03,0.30), brain
 infarcts (OR=1.31;1.06,1.63), lower baseline cognition
 (β=-1.18;-2.01,-0.34), and death (HR=1.13;1.04,1.22). Conclusions
 Dizziness was more consistently associated with neurologic outcomes than
 OH 3-minutes after standing. Delayed OH assessments may miss pathologic
 information related to cerebral injury.
DOI: 10.5061/dryad.hmgqnk9cp
title: Decoupled jaws promote trophic diversity in Cichlid fishes

description: Functional decoupling of oral and pharyngeal jaws is widely considered to
 have expanded the ecological repertoire of cichlid fishes. But, the degree
 to which the evolution of these jaw systems is decoupled and whether
 decoupling has impacted trophic diversification remains unknown. Focusing
 on the large Neotropical radiation of cichlids, we ask whether oral and
 pharyngeal jaw evolution is correlated and how their evolutionary rates
 respond to feeding ecology. In support of decoupling, we find relaxed
 evolutionary integration between the two jaw systems, resulting in novel
 trait combinations that potentially facilitate feeding mode
 diversification. These outcomes are made possible by escaping the
 mechanical trade-off between force transmission and mobility, which
 characterizes a single jaw system that functions in isolation. In spite of
 the structural independence of the two jaw systems, results using a
 Bayesian, state-dependent, relaxed-clock model of multivariate Brownian
 motion indicate strongly aligned evolutionary responses to feeding
 ecology. So, while decoupling of prey capture and processing functions
 released constraints on jaw evolution and promoted trophic diversity in
 cichlids, the natural diversity of consumed prey has also induced a
 moderate degree of evolutionary integration between the jaw systems,
 reminiscent of the original mechanical trade-off between force and
 mobility.
DOI: 10.5061/dryad.stqjq2c0t
title: A Peacock Bass (Cichla) functional novelty relaxes a constraint imposed by the classic cichlid pharyngeal jaw innovation

description: Innovations may provide access to new resources but often result in
 significant trade-offs. Pharyngognathy is a classic pharyngeal jaw
 innovation in which the left and right lower pharyngeal jaw (LPJ) bones
 are united into a single structure, producing a strong bite but reduced
 gape. Throughout cichlids, pharyngeal suturing occurs along the entire
 medial border between LPJ bones, except in Peacock bass (Cichla), where
 these bones are connected by ligaments only in their anterior region. We
 show that this limited attachment permits the jaw bones to spread apart
 and we link this feature to an increase in pharyngeal gape that is
 comparable to non-pharyngognathous species. The capacity of the LPJ bones
 to spread apart is strongest in juveniles and is mostly lost during
 development. Juvenile Cichla exhibit size-specific pharyngeal gape similar
 to non-pharyngognathous percomorphs, but adults exhibit pharyngeal gape on
 par with other predatory cichlids. Relaxation of pharyngeal suturing
 offsets a major deleterious consequence of pharyngognathy by reducing gape
 limitation and we propose this may accelerate the ontogenetic transition
 to piscivory. Partial reversal of the classic cichlid pharyngeal jaw
 innovation highlights the functional trade-offs that often accompany
 innovations and may be a major cause of variation in their
 macroevolutionary consequences.
DOI: 10.5061/dryad.8gtht76km
title: The origin and spread of locally adaptive seasonal camouflage in snowshoe hares

description: Adaptation is central to population persistence in the face of
 environmental change, yet we seldom precisely understand the origin and
 spread of adaptive variation in natural populations. Snowshoe hares (Lepus
 americanus) along the Pacific Northwest (PNW) coast have evolved brown
 winter camouflage through positive selection on recessive variation at the
 Agouti pigmentation gene introgressed from black-tailed jackrabbits (L.
 californicus). Here we combine new and published whole genome and exome
 sequences with targeted genotyping of Agouti in order to investigate the
 evolutionary history of local seasonal camouflage adaptation in the PNW.
 We find evidence of significantly elevated inbreeding and mutational load
 in coastal winter-brown hares, consistent with a recent range expansion
 into temperate coastal environments that incurred indirect fitness costs.
 The genome-wide distribution of introgression tract lengths supports a
 pulse of hybridization near the end of the last glacial maximum, which may
 have facilitated range expansion via introgression of winter-brown
 camouflage variation. However, signatures of a selective sweep at Agouti
 indicate a much more recent spread of winter-brown camouflage. Through
 simulations we show that the delay between the hybrid origin and
 subsequent selective sweep of the recessive winter-brown allele can be
 largely attributed to the limits of natural selection imposed by simple
 allelic dominance. We argue that while hybridization during periods of
 environmental change may provide a critical reservoir of adaptive
 variation at range edges, the probability and pace of local adaptation
 will strongly depend on population demography and the genetic architecture
 of introgressed variation.
description: See accompanying manuscript in The American Naturalist
 (https://doi.org/10.1086/710022) for
 information on data processing.
description: See README.docx file for information on contents of specific
 files.
DOI: 10.34740/kaggle/dsv/14643803
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.kwh70rz15
title: Data from: Roadside diversity in relation to age and surrounding source habitat: evidence for long time lags in valuable green infrastructure

description: 1. The severe and ongoing decline in semi-natural grassland habitat during
 the past two centuries means that it is important to consider how other,
 marginal grassland habitat elements can contribute to landscape-level
 biodiversity, and under what circumstances. 2. To examine how habitat age
 and the amount of core grassland habitat in the surrounding landscape
 affect diversity in green infrastructure, we carried out inventories of 36
 rural road verges that were either historical (pre-1901) or modern
 (established post-1901 and before 1975), and were surrounded by relatively
 high (&gt;15%) or low (&lt;5%) levels of grassland habitat. We
 recorded the number of plant species, grassland specialists, grassland
 conservation species and the fraction of the landscape’s species and
 specialists found in the road verge. 3. Road verge communities were
 characterised by high levels of grassland specialist species (35% of the
 161 species recorded), with road verge sites supporting 15-20% of the
 specialist species found in the surrounding 25 km2 landscape. 4. Richness
 of species and specialists were more closely related to road age than to
 the amount of surrounding habitat. Higher diversity in historical roads,
 despite the majority of modern roads being at least 60 years old, suggests
 a long time lag in the establishment of grassland communities in marginal
 grassland habitats. We identified no effect of historical surrounding land
 use on present day diversity in road verges. 5. Road verge richness was
 not affected by the amount of surrounding grassland. This could be due to
 the relatively low amounts of grassland remaining in all landscapes,
 together with dispersal limitation commonly found in grassland plant
 communities contributing to a potential time lag. 6. We identified road
 verges as potentially very important habitats for grassland communities.
 Because of the high levels of grassland specialists present, these and
 other marginal grasslands and grassland green infrastructure should be
 explicitly considered in landscape-scale conservation management.
 Practitioners looking to identify the most species-rich road verges should
 aim to find the oldest possible, while long time lags in community
 assembly suggests that seed sowing may be appropriate to enhance roadside
 diversity, even in decades-old road verges.
description: See Readme.txt.
DOI: 10.5061/dryad.mgqnk98wp
title: Data from: A new method of Bayesian causal inference in non-stationary environments

description: Bayesian inference is the process of narrowing down the hypotheses
 (causes) to the one that best explains the observational data (effects).
 To accurately estimate a cause, a considerable amount of data is required
 to be observed for as long as possible. However, the object of inference
 is not always constant. In this case, a method such as exponential moving
 average (EMA) with a discounting rate is used to improve the ability to
 respond to a sudden change; it is also necessary to increase the
 discounting rate. That is, a trade-off is established in which the
 followability is improved by increasing the discounting rate, but the
 accuracy is reduced. Here, we propose an extended Bayesian inference
 (EBI), wherein human-like causal inference is incorporated. We show that
 both the learning and forgetting effects are introduced into Bayesian
 inference by incorporating the causal inference. We evaluate the
 estimation performance of the EBI through the learning task of a
 dynamically changing Gaussian mixture model. In the evaluation, the EBI
 performance is compared with those of the EMA and a sequential discounting
 expectation-maximization algorithm. The EBI was shown to modify the
 trade-off observed in the EMA.
description: This includes simulation result data and program source files.
 The program is written in C ++ and uses the Qt library.