cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g1m5
title: Mass estimation of extinct taxa and phylogenetic hypothesis both influence analyses of character evolution in a large clade of birds (Telluraves)

description: Incorporating extinct taxa in phylogenetic comparative methods is rapidly
 becoming invaluable in studies of character evolution. An increasing
 number of studies have evaluated the effects of extinct taxa, and
 different numbers of extinct taxa, on model selection and parameter
 estimation. Body mass is a well-studied phenotype, but individual mass
 estimates may vary dramatically depending on the particular measurement
 used. Here, we perform an analysis of body mass evolution in a large clade
 of principally arboreal birds, incorporating 76 extinct species. We
 evaluate how different methods for estimating body mass of extinct taxa,
 and different phylogenetic hypotheses, affect our understanding of the
 rate and pattern of body mass evolution. Our results show that model
 selection can vary dramatically depending on the phenotypic and
 phylogenetic hypothesis used in the reconstruction. Even small changes in
 phenotype estimates can lead to different model selection and, as a
 result, affect the inferred evolutionary history. The best fit models
 support an increase in the rate of evolution following the K-Pg boundary,
 with variation accumulating linearly through the Cenozoic. These results
 provide additional insight into the application of comparative models of
 evolution, as well as the evolutionary history of one of the most
 spectacular vertebrate radiations.
DOI: 10.5061/dryad.d51c59zxt
title: Data from: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

description: Microtubules are cytoskeletal structures involved in stability, transport
 and organization in the cell. The building blocks, the α- and β-tubulin
 heterodimers, form protofilaments that associate laterally into the hollow
 microtubule. Microtubule also exists as highly stable doublet microtubules
 in the cilia where stability is needed for ciliary beating and function.
 The doublet microtubule maintains its stability through interactions at
 its inner and outer junctions where its A- and B-tubules meet. Here, using
 cryo-electron microscopy, bioinformatics and mass spectrometry of the
 doublets of Chlamydomonas reinhardtii and Tetrahymena thermophila, we
 identified two new inner junction proteins, FAP276 and FAP106, and an
 inner junction-associated protein, FAP126, thus presenting the complete
 answer to the inner junction identity and localization. Our structural
 study of the doublets shows that the inner junction serves as an
 interaction hub that involves tubulin post-translational modifications.
 These interactions contribute to the stability of the doublet and hence,
 normal ciliary motility.
description: Cilia were purified from Chlamydomonas, salt-treated to remove
 outside proteins. The samples were subjected to tandem mass spectrometry
 according to the protocol described in Dai et al. 2019, bioRxiv. (https://doi.org/10.1101/739383)
DOI: 10.5061/dryad.jdfn2z371
title: Altered corticolimbic connectivity reveals sex-specific adolescent outcomes in a rat model of early life adversity

description: Exposure to early-life adversity (ELA) increases the risk for
 psychopathologies associated with amygdala-prefrontal cortex (PFC)
 circuits. While sex differences in vulnerability have been identified with
 a clear need for individualized intervention strategies, the
 neurobiological substrates of ELA-attributable differences remain unknown
 due to a paucity of translational investigations taking both development
 and sex into account. Male and female rats exposed to maternal separation
 ELA were analyzed with anterograde tracing from basolateral amygdala (BLA)
 to PFC to identify sex-specific innervation trajectories through
 juvenility (PD28) and adolescence (PD38;PD48). Resting-state functional
 connectivity (rsFC) was assessed longitudinally (PD28;PD48) in a separate
 cohort. All measures were related to anxiety-like behavior. ELA-exposed
 rats showed precocial maturation of BLA-PFC innervation, with females
 affected earlier than males. ELA also disrupted maturation of female rsFC,
 with enduring relationships between rsFC and anxiety-like behavior. This
 study is the first providing both anatomical and functional evidence for
 sex- and experience-dependent corticolimbic development.
DOI: 10.5061/dryad.v9s4mw6qs
title: Morphology and osteohistology of a large-bodied caenagnathid (Theropoda: Oviraptorosauria) from the Hell Creek Formation (Montana): implications for size-based classifications and growth reconstruction in theropods

description: Oviraptorosaurs, like many coelurosaurians, are frequently diagnosed using
 incomplete or fragmentary skeletal remains, with factors such as body size
 often used to assign material to a particular taxon or as a basis for
 describing new species. Here we describe a partial skeleton, ROM VP 65884,
 from the Hell Creek Formation (Montana), and through morphological and
 phylogenetic comparisons identify it as belonging to Caenagnathidae, and
 likely referable to Anzu wyliei. We perform multi-element
 osteohistological sampling of the tibia, fibula, manual phalanx, rib, and
 gastralium of ROM VP 65884 so as to determine the ontogenetic status of
 the individual, and to perform a detailed assessment of the intra-skeletal
 variation present in a series of histological proxies for growth and
 development. Skeletochronological analysis suggests ROM VP 65884 was still
 actively growing at time of death. Lacunar area was variable, but
 consistent with values reported for other dinosaurs and vertebrates.
 Osteocyte lacunar densities (OLD) were found to be relatively similar to
 the few previous measurements known from coelurosaurian dinosaurs, and
 preserved no ontogenetic pattern. OLD was much higher in sampled rib and
 gastralia elements when compared to limbs, and the high variability in OLD
 overall lends further support against the hypothesis of this feature
 acting as a proxy for mass-specific growth rate. Our results stress the
 importance of using osteohistological analyses to constrain variation and
 permit ontogenetic assessment, and suggest caution be taken when using
 size as a determinant for referral of disassociated elements to specific
 or new coelurosaur taxa.
DOI: 10.82294/dvnbntdsp
title: Entrevistas semiestructuradas. Territorio: Cali. Sector: Educación. Año: 2025

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2025, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Educación (educación formal) en la ciudad de Cali.
DOI: 10.5061/dryad.n8pk0p2r3
title: Environmental decomposition of olefinic cuticular hydrocarbons of Periplaneta americana generates a volatile pheromone that guides social behaviour

description: Once emitted, semiochemicals are exposed to reactive environmental factors
 that may alter them, thus disrupting chemical communication. Some species,
 however, might have adapted to detect environmentally mediated breakdown
 products of their natural chemicals as semiochemicals. We demonstrate that
 air, water vapour and ultraviolet (UV) radiation break down unsaturated
 cuticular hydrocarbons (CHCs) of Periplaneta americana (American
 cockroach), resulting in the emission of volatile organic compounds
 (VOCs). In behavioural assays, nymphs strongly avoided aggregating in
 shelters exposed to the breakdown VOCs from cuticular alkenes. The three
 treatments (air, water vapour, UV) produced the same VOCs, but at
 different time-courses and ratios. Fourteen VOCs from UV-exposed CHCs
 elicited electrophysiological responses in nymph antennae; 10 were
 identified as 2-nonanone, 1-pentanol, 1-octanol, 1-nonanol, tetradecanal,
 acetic acid, propanoic acid, butanoic acid, pentanoic acid and hexanoic
 acid. When short-chain fatty acids were tested as a mix and a blend of the
 alcohols and aldehyde was tested as a second mix, nymphs exhibited no
 preference for control or treated shelters. However, nymphs avoided
 shelters that were exposed to VOCs from the complete 10-compound mix.
 Conditioned shelters (occupied by cockroaches with faeces and CHCs
 deposited on the shelters), which are normally highly attractive to
 nymphs, were also avoided after UV exposure, confirming that breakdown
 products from deposited metabolites, including CHCs,mediate this
 behaviour. Our results demonstrate that common environmental agents
 degrade CHCs into behaviourally active volatile compounds that potentially
 may serve as necromones or epideictic pheromones, mediating group
 dissolution.
description: Each Excel spreadsheet contains a "metadata" tab
 defining the variables.
DOI: 10.5068/d1bm1r
title: Relaxed random walks at scale

description: Relaxed random walk (RRW) models of trait evolution introduce
 branch-specific rate multipliers to modulate the variance of a standard
 Brownian diffusion process along a phylogeny and more accurately model
 overdispersed biological data. Increased taxonomic sampling challenges
 inference under RRWs as the number of unknown parameters grows with the
 number of taxa. To solve this problem, we present a scalable method to
 efficiently fit RRWs and infer this branch-specific variation in a
 Bayesian framework. We develop a Hamiltonian Monte Carlo (HMC) sampler to
 approximate the high-dimensional, correlated posterior that exploits a
 closed-form evaluation of the gradient of the trait data log-likelihood
 with respect to all branch-rate multipliers simultaneously. Our gradient
 calculation achieves computational complexity that scales only linearly
 with the number of taxa under study. We compare the efficiency of our HMC
 sampler to the previously standard univariable Metropolis-Hastings
 approach while studying the spatial emergence of the West Nile virus in
 North America in the early 2000s. Our method achieves at least a 6-fold
 speed-increase over the univariable approach. Additionally, we demonstrate
 the scalability of our method by applying the RRW to study the correlation
 between five mammalian life history traits in a phylogenetic tree with
 3650 tips.
DOI: 10.5061/dryad.44j0zpc90
title: Using stable isotopes to estimate migratory connectivity for a patchily distributed, wetland-associated Neotropical migrant

description: Estimates of migratory connectivity are needed for full annual cycle
 population models of migratory bird species experiencing rapid declines in
 abundance. One technique to determine migratory connectivity is through
 stable isotope analysis. This low-resolution method may be influenced by
 how data are calibrated between isotopes measured in precipitation and
 those measured in feathers, and can be informed by incorporating relative
 abundance into the assignment model. eBird abundance maps are a new tool
 combining citizen science data into a predictive species distribution
 model. In the Prothonotary Warbler (Protonotaria citrea), a
 wetland-associated songbird with a patchy breeding distribution, we sought
 to use stable-hydrogen isotope analysis informed by a species-specific
 calibration equation and eBird abundance data to determine the strength of
 migratory connectivity. We developed a species-specific calibration
 equation using known-origin samples from the breeding grounds and found
 that stable-hydrogen isotope values measured in precipitation explained
 50% of the variation in stable-hydrogen isotope values among feathers. We
 found that the assignment model incorporating eBird abundance data
 correctly identified the true origins of 66% of individuals, and that the
 average assignment area (as a measure of precision) was 64% of the
 breeding distribution. These results represented a 7% increase in
 precision and a 3% decrease in accuracy when compared to a model that was
 not informed by abundance. Based on these models, wintering populations
 from 6 countries represented a mix of likely breeding origins, suggesting
 low migratory connectivity for Prothonotary Warblers. We found evidence
 that wintering latitude was related to likely breeding origin, with
 individuals at western wintering locations more likely to have southern
 breeding origins, but this relationship was weak. These results
 corroborate studies using archival light-level geolocators and
 high-resolution genetic markers, which also demonstrated weak migratory
 connectivity in this species. For patchily distributed species, eBird
 abundance data may not provide a useful increase in precision and accuracy
 for isotope assignments.
description: See manuscript for methodology.
DOI: 10.5061/dryad.6djh9w0x1
title: Extinction of North American Cuvieronius (Mammalia, Proboscidea, Gomphotheriidae) driven by dietary resource competition with sympatric mammoths and mastodons

description: The gomphotheres were a diverse and widespread group of proboscideans
 occupying Eurasia, North America, and South America throughout the
 Neogene. Their decline was temporally and spatially heterogeneous and the
 gomphotheres ultimately became extinct during the late Pleistocene;
 however, the genus Cuvieronius is rarely represented in late Pleistocene
 assemblages in North America. Two alternative hypotheses have been invoked
 to explain this phenomenon: (1) competitive exclusion by sympatric
 mammoths and mastodons, or (2) ecologic displacement due to an
 environmental transition from closed forests to open grasslands. To test
 whether competition for resources contributed to the demise of North
 American Cuvieronius, we present herein a large collection of stable
 isotope and dental microwear data from populations occupying their
 Pleistocene refugium in the Atlantic Coastal Plain. Results suggest that
 Cuvieronius consumed a wide range of resources with variable textural and
 photosynthetic properties and was not specialized on either grasses or
 browse. Further, we document evidence for the consumption of similar foods
 between contemporaneous gomphotheres, mammoths, and mastodons. The
 generalist feeding strategy of the gomphotheres likely facilitated their
 high Miocene abundance and diversity. However, this "jack of all
 trades and master of none" feeding strategy may have proved
 challenging following the arrival of mammoths and likely contributed to
 the extirpation of Cuvieronius in North America.
description: <strong>Supplementary Appendix 1 - Explanation of
 Paleoecological Proxies</strong> An introduction
 and background to the paleoecological proxies used in this analysis, which
 includes (1) dental microwear, (2) stable carbon isotopes, and (3) stable
 oxygen isotopes. Application references included as well as more in-depth
 explanations to some of the nuances which may be observed in the data
 presented within the manuscript.
 <strong>Supplementary Tables 1-2</strong>
 Supplementary Tables 1 and 2, which include (1) the raw specimen
 information and data used in the analyses and (2) a summary of the
 <em>p</em>-values for statistical comparisons amongst
 proboscidean samples. <strong>High-Resolution
 Color Bitmap Images of DMTA Sample Surfaces</strong>
 Includes: (1) <em>Cuvieronius hyodon</em> (Sample #
 TMM 47200-172), (2) <em>Mammut americanum </em>(Sample # UF
 80004), and (3) <em>Mammuthus columbi</em> (Sample # UF
 86825).
DOI: 10.5061/dryad.zs7h44j4p
title: Water-borne and plasma corticosterone are not correlated in spotted salamanders

description: Water-borne hormone measurement is a noninvasive method suitable for
 amphibians of all sizes that are otherwise difficult to sample. For this
 method, containment-water is assayed for hormones released by the animal.
 Originally developed in fish, the method has expanded to amphibians, but
 requires additional species-specific validations. We wanted to determine
 physiological relevance of water-borne corticosterone in spotted
 salamanders (Ambystoma maculatum) by comparing concentrations to those
 taken using established corticosterone sampling methods, such as plasma.
 Using a mixture of field and laboratory studies, we compared water-borne
 corticosterone levels to other traditional methods of sampling
 corticosterone for spotted salamander larvae, metamorphs, and adults.
 Despite multiple attempts, and detecting differences between age groups,
 we found no correlations between water-borne and plasma corticosterone
 levels in any age group. Water-borne sampling measures a rate of release;
 whereas plasma is the concentration circulating in the blood. The unique
 units of measurement may inherently prevent correlations between the two.
 These two methods may also require different interpretations of the data
 and the physiological meaning. We also note caveats with the method,
 including how to account for differences in body size and life history
 stages. Collectively, our results illustrate the importance of careful
 validation of water-borne hormone levels in each species in order to
 understand its physiological significance.
DOI: 10.6073/pasta/394efd37a8262c73f41aab7d404ffd3a
title: Monitoring juvenile Chinook salmon outmigration using rotary screw traps on Deer and Mill creeks 2023 to present

description: The California Department of Fish and Wildlife (CDFW) conducts juvenile salmonid emigration monitoring on Mill and Deer Creek (Tehama County, CA) annually from October through June using rotary screw traps (RSTs). Data from this monitoring is used to estimate juvenile spring-run Chinook salmon (Oncorhynchus tshawytscha) (spring-run) abundance and passage, identify yearling outmigration timing and alert resource agencies of juvenile spring-run presence in the lower Sacramento-San Joaquin Delta. This data will be included in the development of a juvenile production estimate (JPE) for spring-run Chinook salmon in the Sacramento River as required by Condition of Approval 7.5.2 of Incidental Take Permit No. 2081-2019-006-00 (ITP) issued by CDFW to California Department of Water Resources (DWR) for the long-term operation of the State Water Project. Salmonid data collected from the Mill and Deer RSTs, among other datasets, is also used by the Salmon Monitoring Team (SaMT) to understand the movement of juvenile salmon in the Sacramento River Watershed to estimate the number of winter-run and spring-run Chinook salmon that have entered the Sacramento-San Joaquin Delta (Delta). SaMT is a real-time operations monitoring team required by Condition of Approval 8.1.2 of the ITP which meets weekly from October through June, to provide advice for real-time management of SWP operations to DWR, CDFW, and the Water Operation Management Team (WOMT) to minimize take of winter-run and spring-run Chinook salmon in the Delta.
 This data package is complimentary to edi.1504 and represents current RST monitoring on Deer and Mill creeks. Data within the current year’s monitoring season are considered provisional.
DOI: 10.5061/dryad.h70rxwdds
title: Data from: Brassinosteroids act as a positive regulator of NBR1-dependent selective autophagy in response to chilling stress in tomato

description: Autophagy is a highly conserved and regulated catabolic process involved
 in the degradation of protein aggregates, and it plays critical roles in
 eukaryotes. In plants, autophagy has been well studied in stress
 responses. Although multiple molecular processes can induce or suppress
 autophagy, the mechanism of its regulation by phytohormones is poorly
 understood. Brassinosteroids (BRs) are steroid phytohormones that play
 crucial roles in plant response to stresses. In present study, we
 investigate the role of BRs in NBR1-dependent selective autophagy in
 response to chilling stress in tomato. BRs and their signaling element
 BZR1 can induce autophagy and protein accumulation of its selective
 receptor NBR1 in tomato under chilling stress. Cold increased the
 stability of BZR1, which was promoted by BRs. Cold- and BR-induced BZR1
 stability activated the transcription of several ATGs and NBR1 genes by
 directly binding to the promoters of those genes, which resulted in the
 formation of selective autophagy. Furthermore, silencing of these ATGs or
 NBR1 genes resulted in the decreased accumulation of several functional
 proteins and the increased accumulation of ubiquitinated proteins,
 subsequently compromised BR-induced cold tolerance. These results strongly
 suggest that BRs regulate NBR1-dependent selective autophagy by
 BZR1-dependent manner in response to chilling stress in tomato.
DOI: 10.5061/dryad.ncjsxksqn
title: Global biogeographic synthesis and priority conservation regions of the relict tree family Juglandaceae

description: Abstract Aim: To establish a complete database of Juglandaceae at a
 spatiotemporal scale and develop a phylogeographic framework with which to
 elucidate the distributional patterns, diversity patterns, origins,
 evolution, and conservation priority regions of this family. Location:
 Worldwide Methods: Data on the distribution of all the extant and fossil
 species of Juglandaceae were collected, followed by analyses of its
 latitudinal distribution, elevational distribution, and species and
 generic diversity. Furthermore, based on all genera and 87% of the
 species, we reconstructed phylogenetic relationships, estimated divergence
 times, calculated phylogenetic diversity and inferred ancestral
 distributions. Results: Extant Juglandaceae (10 genera and 60 species) are
 mainly distributed in eastern Asia and North America (principally between
 20°N and 40°N). Tropical Juglandaceae mainly inhabit mountainous areas
 higher than 1000 m, especially in the New World. Southwest China and
 northern Vietnam are characterized by high species, generic, and
 phylogenetic diversity. The United States of America has only high species
 diversity. The area of origin of Juglandaceae was North America and Europe
 in the early Eocene, and its widespread dispersal mainly occurred between
 13 and 26 Ma. Main conclusions: The members of Juglandaceae inhabit areas
 with temperate climatic conditions. The diversification centre has shifted
 intercontinentally from North America and Europe to Southwest China and
 northern Vietnam, which are identified as conservation priority regions.
 The high-latitude cooling during the Oligocene followed by a long-term
 stable warmer climate in the early and middle Miocene drove the southward
 translocation of the family.