cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18931zct6
title: Data from: A treasure from the past: former sperm whale distribution in Indonesian waters unveiled using distribution models and historical whaling data

description: Aim: This study is the first in Indonesia to assess historical sperm whale
 (Physeter macrocephalus) seasonal distributions by combining historical
 whaling data with environmental factors associated with sperm whale
 habitat preferences. Since current records of whale occurrence covering
 the whole of Indonesian waters are incomplete, we used historical whaling
 data summarized by Charles Haskins Townsend in 1935 to model its potential
 distribution for each season. Location: Indonesian waters (92-143E,
 9N-14S) Taxa: Sperm whale (Physeter macrocephalus) Methods: We used a
 presence-only habitat model -Maximum Entropy (Maxent)-, and a
 presence-pseudo-absence method -Generalized Additive Model (GAM)- with
 nine submerged topographic variables to predict historical seasonal
 distributions. Results: Both Maxent and GAM predict similar potential
 distribution which align closely with the whaling data. The results
 indicate that in four areas in the eastern part of Indonesia, no seasonal
 differences occurred in sperm whale distribution, while noticeable
 seasonal differences were indicated in other areas. The key parameters
 that characterise sperm whale habitat in both models were distance to
 coast, distance to -1000m and -5000m isobaths, and submarine key features
 such as trough and trench. Main conclusions: The historical catch data of
 this species can be used to describe the historical species distribution
 and provide a baseline to assess present distribution, prioritize current
 research and monitoring, and recommend future data collection. Our models
 also predict distributions that are significantly larger than the ones
 occupied by sperm whales nowadays, another example of a shifting baseline.
 Our study demonstrates the benefits of incorporating historical whaling
 data into habitat models for ecological investigation and to inform
 conservation efforts for cetaceans.
description: The original data are available from Townsend (1935) through the
 permission from New Bedford Whaling Museum. We proceeded the original data
 by converting the data into a raster format using ArcGIS
 10.6.1.
DOI: 10.5061/dryad.tqjq2bvvz
title: Data from: Heat dissipation capacity influences reproductive performance in an aerial insectivore

description: Climatic warming is predicted to increase the frequency of extreme weather
 events, which may reduce an individual's capacity for sustained
 activity due to thermal limits. We tested whether the risk of overheating
 may limit parental provisioning of an aerial insectivorous bird in
 population decline. For many seasonally breeding birds, parents are
 thought to operate close to an energetic ceiling during the 2-3 week
 chick-rearing period. The factors determining the ceiling remain unknown,
 although it may be set by an individual 's capacity to dissipate body
 heat (the heat dissipation limitation hypothesis). Over two breeding
 seasons we experimentally trimmed the ventral feathers of female tree
 swallows (Tachycineta bicolor, Vieillot, 1808) to provide a thermal
 window. We then monitored maternal and paternal provisioning rates,
 nestling growth rates, and fledging success. We found the effect of our
 experimental treatment was context-dependent. Females with an enhanced
 capacity to dissipate heat fed their nestlings at higher rates than
 controls when conditions were hot, but the reverse was true under cool
 conditions. Control females and their mates both reduced foraging under
 hot conditions. In contrast, male partners of trimmed females maintained a
 constant feeding rate across temperatures, suggesting attempts to match
 the feeding rate of their partners. On average, nestlings of trimmed
 females were heavier than controls, but did not have a higher probability
 of fledging. We suggest that removal of a thermal constraint allowed
 females to increase provisioning rates, but additionally provided
 nestlings with a thermal advantage via increased heat transfer during
 maternal brooding. Our data provide support for the heat dissipation
 limitation hypothesis and suggest that depending on temperature, heat
 dissipation capacity can influence reproductive success in aerial
 insectivores.
description: The attached files contain the necessary descriptions for
 understanding and working with data used in the construction of Tapper et
 al. 2020 (Journal of Experimental Biology). The JEB_dryad_readme.docx file
 contains descriptions of each file name attached to this data repository,
 and descriptions of the data contained within each column of a data file.
 Information pertaining to the R code, which has been provided in this data
 repository as a .Rmd (R Markdown) file, has not been provided within this
 readme file, because necessary descriptions for understanding our code are
 provided within the R code file itself.
DOI: 10.5061/dryad.9p8cz8wcz
title: Data from: Little giants: a rapidly invading seagrass alters ecosystem functioning relative to native foundation species

description: The spread of invasive species is a major component of global ecological
 change and how and when to manage particular species is a diicult
 empirical question. Ideally, these decisions should be based on the
 speciic impacts of invading species including both their efects on native
 competitors and how they may or may not play similar roles in broader
 ecosystem functioning. Halophila stipulacea is an invasive seagrass
 currently spreading through the Caribbean, and as seagrasses are
 foundation species, the efects of invasion have the potential to be
 particularly far-reaching. To evaluate the impacts of H. stipulacea we
 quantiied spread and potential for displacement of native seagrasses as
 well as the efects of invasion on multiple ecosystem processes,
 particularly resource support for higher trophic levels and habitat
 creation. Long-term monitoring suggested that H. stipulacea likely
 displaces some native seagrasses (Syringodium filiforme and Halodule
 wrightii), but not others. Halophila stipulacea had lower N and protein
 levels and higher C:N ratios than native seagrasses, and as such is a
 poorer quality resource for consumers. We also observed signiicantly lower
 consumption of H. stipulacea than the native S. filiforme but limited
 diferences compared to Thalassia testudinum. We found H. stipulacea
 created a more nutrient limited environment than T. testudinum and there
 were signiicantly distinct invertebrate assemblages in native- and
 invasive- dominated seagrass beds, but no diference in species richness or
 invertebrate biomass. These results suggest that the spread of H.
 stipulacea would impact a variety of ecological processes, potentially
 restructuring seagrass ecosystems through both direct impacts on
 environmental conditions (e.g., nutrient availability) and indirect food
 web interactions.
DOI: 10.15468/dl.yhwzfh
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (PDD 91700, PDD 91659)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002353-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4b8gtht93
title: Data from: Boron application increases growth of Brazilian Cerrado grasses

description: Nutrients are known to limit productivity of plant communities around the
 world. In the Brazilian Cerrado, indirect evidences point to phosphorus as
 the main limiting nutrient, but some fertilization experiments suggest
 that one or more micronutrients might play this role. Boron is one of the
 essential micronutrients for plants. Agronomically, it received some
 attention, but it has mostly been neglected in ecological studies
 assessing the effects of nutrients on plant growth. Through field
 fertilization and mesocosm experiments, we show that boron addition
 increased biomass production of Cerrado herbaceous vegetation. This could
 be related to a lower aluminium uptake in the boron fertilized plants.
 Even considering that plant growth was promoted by boron addition due to
 aluminium toxicity alleviation, this is the first study reporting boron
 limitation in natural, non-cultivated plant communities, and also the
 first report of this kind in vegetative grasses. These results contribute
 to disentangling patterns of nutrient limitation among plant species of
 the species-rich, aluminium-rich and nutrient-poor Cerrado biome, and
 highlight the potential role of micronutrients, such as boron, for growth
 of non-crop plants. Understanding how nutrient limitation differs amongst
 functional groups in the highly biodiverse areas founded on ancient
 tropical soils may help managing these plant communities in a changing
 world.
DOI: 10.15468/dl.fu5t5h
title: Occurrence Download

description: A dataset containing 6755 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Themisto gaudichaudii",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 6755 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002352-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d7wm37pz7
title: Data from: Long-lived marine species may be resilient to environmental variability through a temporal portfolio effect

description: Maintenance of a portfolio of adaptive alleles may provide resilience of
 populations to natural environmental variability. We used Pacific ocean
 perch (POP; Sebastes alutus) to test for the maintenance of adaptive
 variation across overlapping generations. POP are a long-lived species
 characterized by widespread larval dispersal in their first year and a
 longevity of over 100 years. In order to understand how early marine
 dispersal affects POP survival and population structure, we used
 Restriction Site Associated DNA sequencing (RADseq) to obtain 11,146
 single-nucleotide polymorphisms (SNPs) from 401 young-of-the-year (YOY)
 POP collected during surveys conducted in 2014 (19 stations) and 2015 (4
 stations) in the eastern Gulf of Alaska. Population clustering analysis
 showed that the POP samples represented four distinct ancestral
 populations mixed throughout the sampling area. Based on prior work on
 larval dispersal of POP, these larvae are most likely from distinct
 parturition locations that are mixing during their pelagic dispersal life
 stage. Latent factor mixed models revealed that POP larvae face
 significant selection during their first year at sea, which were specific
 to the year of their birth. Thus each adult cohort’s genetic composition
 is heavily influenced by the environmental conditions experienced during
 their first year at sea. Long-lived species relying on broadcast spawning
 strategies may therefore be uniquely resilient to environmental
 variability by maintaining a portfolio of cohort-specific adaptive
 genotypes, and age truncation due to overfishing of older cohorts may have
 detrimental effect on the population viability.
description: Young-of-the-year Pacific
 ocean perch (Sebastes alutus) were collected during NOAA oceanographic
 surveys in the summer of 2014 (July 8 to August 14) and 2015 (July 13 to
 July 22). The larvae and young of the year fish were distinguished from
 congenerics using diagnostic SNPs prior to inclusion in this study. The
 resulting sample size of identified YOY POP was 399 fish in 2014 and 108
 in 2015. Fish
 length, weight, and lipid content for each identified POP fish were
 measured at Auke Bay Laboratories in Juneau, AK.  For DNA analysis, a
 small tissue plug was extracted through an incision in the abdominal wall
 that included the heart tissue and stored in 95% ethanol. RADseq library preparation was
 done for 513 samples including eight samples that were replicates using
 the Sbf1 restriction enzyme and 150 bp paired end sequencing was done on
 two lanes using Illumina HiSeq 4000.
description: Note that the prepared sample size and the recovered sample size
 are slightly different due to no DNA recovered in a couple of plate
 wells.
DOI: 10.82294/dvneepned
title: Observaciones semiestructuradas. Territorio: Norte de Santander. Eje medular: Agenciamiento. Sector: Cultura. Año: 2025

description: La capacidad de agencia o agenciamiento se entiende como las libertades y oportunidades que tiene un individuo para tomar decisiones y actuar en un contexto, transformando situaciones que afectan a su comunidad a nivel social y ambiental. Implica la capacidad de razonar críticamente y llevar a cabo acciones intencionales. En el ámbito de la educación artística y ambiental, esto se manifiesta en la capacidad de realizar el potencial creativo y de contribuir a la construcción de una realidad institucional o social (Maras, 2018; Katz-Buonicontro, 2018; García-Calvo y Garzón-Barragán, 2023).
DOI: 10.5061/dryad.f1vhhmgtc
title: Chromosome 28 genotypes and phenotypes for all samples used in the analyses, full panel of 298 genotypes, and R script for R-squared values

description: Recent studies have begun to elucidate the genetic basis for phenotypic
 traits in salmonid species, but many questions remain before these
 candidate genes can be directly incorporated into conservation management.
 In Chinook Salmon (Oncorhynchus tshawytscha), a region of major effect for
 migration timing has been discovered that harbors two adjacent candidate
 genes (greb1L, rock1), but there has been limited work to examine the
 association between these genes and migratory phenotypes at the
 individual, compared to the population, level. To provide a more thorough
 test of individual phenotypic association within lineages of Chinook
 Salmon, 33 candidate markers were developed across a 220 Kb region on
 chromosome 28 previously associated with migration timing. Candidate and
 neutral markers were genotyped in individuals from representative
 collections that exhibit phenotypic variation in timing of arrival to
 spawning grounds from each of three lineages of Chinook Salmon.
 Association tests confirmed the majority of markers on chromosome 28 were
 significantly associated with arrival timing and the strongest association
 was consistently observed for markers within the rock1 gene and the
 intergenic region between greb1L and rock1. Candidate markers alone
 explained a wide range of phenotypic variation for Lower Columbia and
 Interior ocean-type lineages (29% and 78%, respectively), but less for the
 Interior stream-type lineage (5%). Individuals that were heterozygous at
 markers within or upstream of rock1 had phenotypes that suggested a
 pattern of dominant inheritance for early arrival across populations.
 Finally, previously published fitness estimates from the Interior
 stream-type lineage enabled tests of association with arrival timing and
 two candidate markers, which revealed that fish with homozygous mature
 genotypes had slightly higher fitness than fish with premature genotypes,
 while heterozygous fish were intermediate. Overall, these results provide
 additional information for individual-level genetic variation associated
 with arrival timing that may assist with conservation management of this
 species.
DOI: 10.5061/dryad.51c59zw5b
title: Selecting and averaging relaxed clock models in Bayesian tip dating of Mesozoic birds

description: Relaxed clock models are fundamental in Bayesian clock dating, but a
 single distribution characterizing the clock variation is typically
 selected. Hence, I developed a new reversible-jump Markov chain Monte
 Carlo (rjMCMC) algorithm for drawing posterior samples between the
 independent lognormal (ILN) and independent gamma rates (IGR) clock
 models. The ability of the rjMCMC algorithm to infer the true model was
 verified through simulations. I then applied the algorithm to the Mesozoic
 birds data previously analyzed under the white noise (WN) clock model. In
 comparison, averaging over the ILN and IGR models provided more reliable
 estimates of the divergence times and evolutionary rates. The ILN model
 showed slightly better fit than the IGR model and much better fit than the
 autocorrelated lognormal (ALN) clock model. When the data were
 partitioned, different partitions showed heterogeneous model fit for ILN
 and IGR clocks. The implementation provides a general framework for
 selecting and averaging relaxed clock models in Bayesian dating analyses.
description: Please see the Method section of the paper.
description: 1. dataS1_simulations.zip: this zip archive contains<br>
  (1) 100 birth-death trees generated by TreeSim in R (bd.trees and
 sim.bd.r); <br>  (2) source code of the simulator (src/
 folder);<br>  (3) shell script of each simulation setting in
 individual folders.<br>  <br> 2. dataS2_birds.zip: this zip
 archive contains MrBayes commands for<br>  (1) the morphological
 data matrix (birds.nex);<br>  (2) stepping-stone sampling under the
 IGR clock model (ss_igr)<br>  (3) stepping-stone sampling under the
 ILN clock model (ss_igr)<br>  (4) stepping-stone sampling under the
 ALN(TK02) clock model (ss_aln)<br>  (5) rjMCMC sampling for
 unpartitioned data (td_mix)<br>  (6) rjMCMC sampling for partitioned
 data (td_p6_mix)
DOI: 10.5061/dryad.02v6wwq0s
title: Phenotypic divergence in two sibling species of shorebird: Common Snipe and Wilson's Snipe (Charadriiformes: Scolopacidae)

description: Natural selection and social selection are among the main shapers of
 biological diversity, but their relative importance in divergence remains
 understudied.  Additionally, although neutral
 evolutionary processes may promote phenotypic divergence, their potential
 contribution in speciation is often overlooked in studies of comparative
 morphology.  In this study, we investigated phenotypic
 differentiation in two allopatric shorebirds: the Palearctic Common
 Snipe Gallinago gallinago and the Nearctic Wilson’s
 Snipe G. delicata.  Specimens of Common Snipe
 (n = 355 skins, n = 163 skeletons) and Wilson’s Snipe (n = 403 skins, n =
 141 skeletons) in natural history collections, were examined to quantify
 differences in skeletal and external measurements, and measures on wing
 and tail plumage variables.  The species did not differ
 in skeletal variables except for the relatively larger sternum of the
 Common Snipe.  The two species do not differ in
 multivariate wing size or shape
 (pointedness).  Previously known plumage differences
 between these species were confirmed: the Common Snipe has fewer
 rectrices, longer and wider outermost rectrices, more extensive white on
 tips of the secondary feathers, and more white in the
 axillaries.  Between-species variance in skeleton,
 primary length, and plumage variables was greater than expected if drift
 was mainly responsible for phenotypic divergence, suggesting a role
 of selective processes.  However, drift could
 not be rejected after adjusting for multiple
 comparisons.  Differences in plumage traits were greater
 than in skeletal or external measurements.  Because
 snipe use plumage traits in signalling, the results suggest a faster
 divergence between these species in socially selected traits than in those
 related to resource use.
description: Phenotypic data of Common Snipe and Wilson's
 Snipe Data collected from museum specimens.
DOI: 10.5061/dryad.tqjq2bvw0
title: Data from: Cdk8 is required for establishment of H3K27me3 and gene repression by Xist and mouse development

description: We previously identified the cyclin dependent kinase Cdk8 as a putative
 silencing factor for Xist. To investigate its role in X inactivation, we
 engineered a Cdk8 mutation in mouse embryonic stem cells (ESCs) carrying
 an inducible system for studying Xist function. We find that Xist
 represses X-linked genes to half the expression level in Cdk8 mutant
 cells, whereas near complete silencing is observed in controls. Lack of
 Cdk8 impairs Ezh2 recruitment and establishment of histone H3 lysine 27
 tri-methylation but not PRC1 recruitment by Xist. Transgenic expression of
 wild-type but not catalytically inactive Cdk8 restores efficient gene
 repression and PRC2 recruitment. Mutation of the paralogous kinase Cdk19
 does not affect Xist function and combined mutations of Cdk8 and Cdk19
 resemble the Cdk8 mutation. In mice a Cdk8 mutation causes
 post-implantation lethality. We observe that homozygous Cdk8 mutant female
 embryos show a greater developmental delay than males on day 10.5.
 Together with inefficient repression of X-linked genes in differentiating
 Cdk8 mutant female ESCs these data show a requirement of Cdk8 for the
 initiation of X inactivation.
description: Microscopy pictures of embryos were taken and image segmentation
 was performed as explained in the journal article. The embryo sizes were
 determined in pixel as indicated for each embryo in the PDF files. For
 each litter a CSV formatted table is provided with all embryo sizes of the
 litter. The dataset contains details of intermediates of image processing,
 and all measurements of embryo size that were used in the study for embryo
 size calculations.
description: To use this dataset the journal article in Development should be
 consulted. In particluar, the Python scripts used for image processing,
 and statistical analysis of measurements are provided in Data S1 and Table
 S4 accompanying the journal article.
DOI: 10.5061/dryad.2jm63xskv
title: Visitor patterns for n-ary data sets

description: Visitor design patterns decouples the data structure and the algorithms.
 Traversal could be in-order or post-order. Applications include sorting
 such as binary sort in O(log n) complexity. The tree and maze illustrate a
 dichotomy in software and systems infrastructure. They are essential
 ingredients in an ecosystem. Use cases include the rationalization of
 taxonomies/thesauri and cognitive biases. Eg. man-woman, snakes-ladders,
 import-export, left-right, train-test.
DOI: 10.15468/dl.9thgc5
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apurimacia boliviana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 81 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002355-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.