cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vt4b8gtp5
title: Shifting ecosystem connectivity during the Pleistocene drove diversification and gene-flow in a species-complex of Neotropical birds (Tityridae: Pachyramphus)

description: Aim: We aim to test the biogeographic drivers of diversification and
 gene-flow at the Isthmus of Panama using a species complex of suboscine
 birds as a case study. We specifically evaluate whether diversification in
 these birds is better explained by continuous parapatry or a Refuge Model
 of periodic isolation and gene-flow due glacial cycling. Location: The
 Isthmus of Panama (Neotropics) Taxon: Pachyramphus aglaiae and P.
 homochrous (Aves: Tityridae) Methods: We develop an approach to
 distinguish among the two biogeographic hypotheses –parapatric ecological
 speciation versus climatically-mediated speciation– by making explicit
 predictions for demographic history, niche evolution, and change in
 geographic connectivity over time. We sequenced genome-wide markers
 (ultraconserved elements) to estimate the evolutionary and demographic
 history of this group. We applied both phylogenomic network analyses and
 demographic modeling using a supervised machine learning approach. These
 genetic analyses were combined with a novel distribution modeling method
 that estimates the probability of interspecies contact as a function of
 climatic conditions through time. Results: We found that both spatial and
 genetic analyses revealed concordant results. All speciation events
 occurred during the Pleistocene and were characterized by non-continuous
 gene-flow, supporting a scenario of climate-mediated diversification.
 Spatial connectivity was highest at present, consistent with our best
 demographic model of secondary contact. Main Conclusions: This study
 exemplifies a mechanism by which speciation, dispersal, and introgression
 unfold in an important region for Neotropical diversification –the Isthmus
 of Panama– where periods of both isolation and introgression probably
 drive diversification. Overall, our results are consistent with the Refuge
 Model of biotic diversification, but suggest that introgression may be a
 crucial yet underappreciated component of this classic paradigm.
description: Here we deposit the cleaned illumina reads from ultraconserved
 element sequencing in addition to mitochondrial genome
 alignments.
DOI: 10.5061/dryad.7h44j0zrb
title: Pat Creek Restoration Project

description: In 2019, the Southeast Alaska Watershed Coalition restored habitat for
 salmon and steelhead trout in Wrangell, Alaska's Pats Creek.
 Thirty-one whole trees were harvested and placed in the mainstem and west
 fork of Pats creek to enhance fish habitat. An abandoned logging road on
 the south side of Pats Creek was breached in four locations to reactivate
 stranded floodplain and restore natural channel migration, and five fish
 passage barriers were removed by the decommissioning of the Tunnel Road.
 Post construction monitoring showed that implementation was in line with
 design plans.  
description: Includes are pre and post construction reports completed by
 Interfluve, Inc. for the project including stream profile surveys. 
 Methods are explained in attached documents.  
description: Citation of uploaded data should credit: 
 Miller, Dan.  2017.  Technical Memorandum:  Pat Creek Design
 Memorandum.  Inter-fluve, Inc.  Brunfelt, Mike and Dan
 Miller.  2019.  Technical Memorandum:  Pat Creek Construction Report. 
 Inter-fluve, Inc.
DOI: 10.5061/dryad.6djh9w0xk
title: Ambient temperature and female body condition are related to night incubation behavior in wood ducks (Aix sponsa)

description: For many animals, parental care behavior is an important aspect of their
 life history that affects both parents and offspring. In birds, one of the
 most important parental care behaviors is incubation, which is costly to
 the parent but directly influences embryonic development and fitness of
 offspring. Some birds exhibit the intriguing behavior of partially
 incubating their eggs prior to clutch completion for only a portion of
 each day. This partial incubation is characterized by lower incubation
 temperatures and constancy than during full-time incubation, which
 typically begins at clutch completion. Partial incubation may preserve the
 viability of eggs laid early in the laying sequence, shorten the length of
 the full incubation period, and/or provide a favorable microclimate to the
 incubating parent. It might also reduce the probability of nest predation,
 nest site takeover by another bird, brood parasitism, and/or predation of
 the adult. Although there is evidence that partial incubation is an
 adaptive behavior and that time invested in this behavior varies among
 individuals of the same species, nothing is known about what may drive
 this inter-individual variation. To investigate how environmental and
 parental characteristics may be related to partial incubation behavior, we
 studied the partial incubation behavior of wood ducks (Aix sponsa) using
 artificial egg temperature loggers within nest boxes. Our results suggest
 that females with greater mass relative to their structural size invest
 more time in partial incubation. Additionally, the incubation temperature
 and length of on-bouts of partial incubation increased over the course of
 the partial incubation period, and ambient temperature during on-bouts was
 positively related to incubation temperature. Ultimately, our study
 suggests that characteristics of both the environment and parent may
 influence the partial incubation behavior of wood ducks, and improves our
 understanding of an important, but understudied, aspect of avian parental
 care.
DOI: 10.82294/dvnukdcrh
title: Observaciones semiestructuradas. Territorio: Cundinamarca. 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.m63xsj3z9
title: Data from: Selection and constraints in the ecomorphological adaptive evolution of the skull of living Canidae (Carnivora, Mammalia)

description: The association between phenotype and ecology is essential for
 understanding the environmental drivers of morphological evolution. This
 is a particularly challenging task when dealing with complex traits such
 as the skull, where multiple selective pressures are at play and evolution
 might be constrained by ontogenetic and genetic factors. In the present
 contribution I integrate morphometric tools, comparative methods and
 quantitative genetics to investigate how ontogenetic constraints and
 selection might have interacted during the evolution of the skull in
 extant Canidae. The results confirm that the evolution of cranial
 morphology was largely adaptive and molded by changes in diet composition.
 While the investigation of the adaptive landscape reveals two main
 Selective Lines of Least Resistance (one associated with size and one
 associated with functional shape features), rates of evolution along size
 were higher than those found for shape dimensions, suggesting the
 influence of constraints on morphological evolution. Structural Modeling
 Analyses revealed that size, which is the line of most genetic/phenotypic
 variation, might have acted as a constraint, negatively impacting dietary
 evolution. Constraints might have been overcome in the case of selection
 for the consumption of large prey, by associating strong selection along
 both size and shape directions. The results obtained here show that
 microevolutionary constraints may have played a role in shaping
 macroevolutionary patterns of morphological evolution.
description: Morphometric data was collected using a Microscribe.
description: <strong>Table of species dietary
 data</strong> Dietary data based on semantic
 analysis of the literature. Contains 13 dietary categories for 40 canid
 species. File- diet.csv  
 <strong>Table of Genebank accession numbers for analyzed
 genes</strong> Table containing the accession
 number for the genes used in the dating of the phylogenetic tree. Contains
 genetic information for 38 canid species plus 4 outgroups.
 File- genes.xls  
 <strong>Canidae phylogeny</strong>
 Dated phylogeny used in all comparative analysis.
 File- dated_canidae.tree  
 <strong>Average measures for each
 species</strong> Mean values for each
 log-measurement for each species. Contain 40 measurements for 39
 species. File- means.xls  
 <strong>Phenotypic covariance matrix for morphometric
 traits</strong> 40x40 covariance P matrix for the
 within-group pattern of co/variation. File-
 W.xlsx   <strong>Morphological
 vectors associated to ecological change</strong>
 Diet-specific
 morphological changes (Δz<sub>diet</sub>) and selection
 gradients (β<sub>diet</sub>)
 File- ecoV.xlsx  
 <strong>Factors controlled</strong>
 Table containing formulas used in the linear models used to
 control for sources of within-species patterns of variation before
 calculating patterns of within-group covariance. File-
 factors_.csv
DOI: 10.5061/dryad.q573n5tfk
title: Data from: Defense against predators incurs high reproductive costs for the aposematic moth Arctia plantaginis

description: To understand how variation in warning displays evolves and is maintained,
 we need to understand not only how perceivers of these traits select
 colour and toxicity, but also the sources of the genetic and phenotypic
 variation exposed to selection by them. We studied these aspects in the
 wood tiger moths Arctia plantaginis which has two locally co-occurring
 male colour morphs in Europe; yellow and white. When threatened, both
 morphs produce defensive secretions from their abdomen and from thoracic
 glands. Abdominal fluid has shown to be more important against
 invertebrate predators than avian predators and the defensive secretion of
 the yellow morph is more effective against ants. Here we focused on the
 morph-linked reproductive costs of secretion of the abdominal fluid and
 quantified the proportion of phenotypic and genetic variation in it. We
 hypothesized that if yellow males pay higher reproductive costs for their
 more effective aposematic display, the subsequent higher mating success of
 white males could offer one explanation for the maintenance of the
 polymorphism. We first found that the heritable variation in the quantity
 of abdominal secretion was very low (h2 = 0.006) and the quantity of
 defensive secretion was not dependent on the male morph. Secondly,
 deploying the abdominal defensive secretion decreased the reproductive
 output of both colour morphs equally. This suggests that potential costs
 of pigment production and chemical defence against invertebrates is not
 linked in A. plantaginis. Furthermore, our results indicate that
 environmentally induced variation in chemical defence can alter an
 individual’s fitness significantly.
description: Data sets include: - Pedigree data used to
 analyse h2 of the abdominal defensive secretion of Arctia plantaginis male
 moths (Pedigree data for the h2 analyses of abdominal defensive secretions
 of Arctia plantaginis males). -Experimental data to
 test the reproductive costs of responsive defence in the Arctia
 plantaginis male moths (A. plantaginis_Cost of defence
 experiment_Phenotypic data). -Behavioural data for the
 Suppelementary information of the manuscript about the defensive behaviour
 of male moths (Supplementary Data for the Figure S1_The amount of
 defensive fluid released under repetitive attacks; Supplementary Data for
 the Figure S2_Quantity of deployed fluid under repetitive
 attacks).  - Natural history data about the defensive
 behaviour from the wild A. plantaginis populations from Southern Finland
 populations (Volumes of defensive fluid collected from the wild Arctia
 plantaginis populations).
DOI: 10.5061/dryad.j3tx95x9c
title: Sphaerospora molnari (Myxozoa) SMBS transcriptome data

description: Parasites employ proteases to evade host immune systems, feed and
 replicate and are often the target of anti-parasite strategies to disrupt
 these interactions. Myxozoans are obligate cnidarian parasites,
 alternating between invertebrate and fish hosts. They are highly divergent
 from other metazoans with regard to their gene sequences, and available
 genomic and transcriptomic datasets are limited. Some myxozoans are
 important aquaculture pathogens such as Sphaerospora molnari replicating
 in the blood of farmed carp before reaching the gills for sporogenesis and
 transmission. Proliferative stages cause a massive systemic lymphocyte
 response and the disruption of the gill epithelia by spore-forming stages
 leads to respiratory problems and mortalities. In the absence of
 a S. molnari genome, we utilized a de
 novo approach to assemble the first transcriptome of
 proliferative myxozoan stages to identify S. molnari proteases that are
 upregulated during the first stages of infection when the parasite
 multiplies massively, rather than in late spore-forming plasmodia.
 Furthermore, a subset of orthologs was used to characterize 3D structures
 and putative druggable targets. An assembled and host filtered
 transcriptome containing 9436 proteins, mapping to 29 560 contigs was
 mined for protease virulence factors and revealed that cysteine proteases
 were most common (38%), at a higher percentage than other myxozoans or
 cnidarians (25-30%). Two cathepsin Ls that were found upregulated in
 spore-forming stages with a presenilin like aspartic protease and a
 dipeptidyl peptidase. We also identified downregulated proteases in the
 spore-forming development when compared with proliferative stages
 including an astacin metallopeptidase and lipases (qPCR). In total, 235
 transcripts were identified as putative proteases using a MEROPS
 database. In silico analysis of highly transcribed
 cathepsins revealed potential drug targets within this data set that
 should be prioritised for development. In silico surveys for proteins are
 essential in drug discovery and understanding host-parasite interactions
 in non-model systems. The present study of S. molnari’s protease arsenal
 reveals previously unknown proteases potentially used for host
 exploitation and immune evasion. The pioneering dataset serves as a model
 for myxozoan virulence research, which is of particular importance as
 myxozoan diseases have recently been shown to emerge and expand
 geographically, due to climate change.
description: Illumina Hi Seq, Host and parasite filtered based on reads and
 assembled transcripts.
DOI: 10.5061/dryad.cjsxksn33
title: Composite landscape predictors improve distribution models of ecosystem types

description: Aim: Distribution modelling is a useful approach to obtain knowledge about
 the spatial distribution of biodiversity, required for e.g., red list
 assessments. While distribution modelling methods have been applied mostly
 to single species, modelling of communities and ecosystems (EDM;
 ecosystem-level distribution modelling) produces results that are more
 directly relevant for management and decision-making. Although the choice
 of predictors is a pivotal part of the modelling process, few studies have
 compared the suitability of different sets of predictors for EDM. In this
 study, we compare the performance of 50 single environmental variables
 with that of 11 composite landscape gradients (CLGs) for prediction of
 ecosystem types. The CLGs represent gradients in landscape element
 composition derived from multivariate analyses, e.g., ‘inner-outer coast’
 and ‘land use intensity’. Location: Norway. Methods: We used data from
 field-based ecosystem type mapping of nine ecosystem types, and
 environmental variables with a resolution of 100×100 m. We built nine
 models for each ecosystem type with variables from different predictor
 sets. Logistic regression with forward selection of variables was used for
 EDM. Models were evaluated with independently collected data. Results:
 Most ecosystem types could be predicted reliably, although model
 performance differed among ecosystem types. We identified significant
 differences in predictive power and model parsimony across models built
 from different predictor sets. Climatic variables alone performed poorly,
 indicating that the current climate alone is not sufficient to predict the
 current distribution of ecosystems. Used alone, the CLGs resulted in
 parsimonious models with relatively high predictive power. Used together
 with other variables, they consistently improved the models. Main
 conclusions: We argue that the use of composite variables as proxies for
 complex environmental gradients has the potential to improve predictions
 from EDMs and thus to inform conservation planning as well as improve the
 precision and credibility of red lists and global change assessments.
description: See description in article (main text and supplementary
 material).
description: The available scripts are general scripts, and can be adapted to
 any ecosystem type (or other modelling targets). The R working directory
 and reference to the specific predictors applied in a study should be set
 specifically in the scripts. The training data for the response variables
 (i.e. ecosystem types) and the spatial data not uploaded here (i.e., the
 climatic and non-climatic ‘basic’ predictor variables) is available on
 request from the authors. Due to the restrictions with ownership of the
 original area frame survey data (AR18X18), these data are not openly
 available from the authors.
DOI: 10.5061/dryad.573n5tb48
title: The seventh macronutrient: how sodium shortfall ramifies through populations, food webs, and ecosystems

description: Of the 25 elements required to build most organisms, sodium has a unique
 set of characteristics that ramify through terrestrial ecology. In plants,
 sodium is found in low concentrations and has little metabolic function;
 in plant consumers, particularly animals, sodium is essential to running
 costly Na-K ATPases. Here I synthesize a diverse literature from
 physiology, agronomy, and ecology, toward identifying sodium’s place as
 the “7th macronutrient”, one whose shortfall targets two trophic
 levels—herbivores and detritivores. I propose that sodium also plays a
 central, though unheralded role in herbivore digestion, via its importance
 to maintaining microbiomes and denaturing tannins. I highlight how sodium
 availability is a key determinant of consumer abundance and the geography
 of herbivory and detritivory. And I propose a re-appraisal of the
 assumption that, because sodium is metabolically unimportant to most
 plants, it is of little use. Instead, I suggest that sodium’s critical
 role in limiting herbivore performance makes it a commodity used by plants
 to manipulate their herbivores and mutualists, and by consumers like bison
 and elephants to generate grazing lawns: dependable sources of sodium.
description: Figure 2 combines published datasets (Na Grassland Soils, NA
 grassland grasses, NA grassland forbs, Borer et al plant species) and two
 literature searches, one on "sodium, invertebrates" (for
 Invertebrates), and one on "sodium, urine" (for Animal Urine).
 All values were converted to Na ppm. 
description: In addition to the Excel file
 "Kaspari_NaVariation_EcologyLetters", there is a word doc with
 metadata describing sources of information, "Metadata for
 Kaspari"
DOI: 10.15468/dl.daup33
title: Occurrence Download

description: A dataset containing 17991 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-180 -60,-70 -60,-70 70,-180 70,-180 -60))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (e9f60bdb-217d-4b4e-a22a-2781321220a1, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 4aaf1825-3ebd-4943-87a3-f67552d468f1, c54097e6-0972-4acb-b849-eaeba29c917d, 750a8724-fa66-4c27-b645-bd58ac5ee010, 1928bdf0-f5d2-11dc-8c12-b8a03c50a862, 28eb1a3f-1c15-4a95-931a-4af90ecb574d)",
 "TaxonKey is Megaptera novaeangliae",
 "Year 2000-2026"
 ]
}

 The dataset includes 17991 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002283-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tqjq2bvvr
title: Data from: Persistent firing in LEC III neurons is differentially modulated by learning and aging

description: Whether and how persistent firing in lateral entorhinal cortex layer III
 (LEC III) supports temporal associative learning is still unknown. In this
 study, persistent firing was evoked in vitro from LEC III neurons from
 young and aged rats that were behaviorally naïve or trained on trace
 eyeblink conditioning. Persistent firing ability from neurons from
 behaviorally naïve aged rats was lower compared to neurons from young
 rats. Neurons from learning impaired aged animals also exhibited reduced
 persistent firing capacity, which may contribute to aging-related learning
 impairments. Successful acquisition of the trace eyeblink task, however,
 increased persistent firing ability in both young and aged rats. These
 changes in persistent firing ability are due to changes to the
 afterdepolarization, which may in turn be modulated by the postburst
 afterhyperpolarization. Together, these data indicate that successful
 learning increases persistent firing ability and d ecreases in persistent
 firing ability contribute to learning impairments in aging.