cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.31zcrjds6
title: Angiosperms follow a convex trade-off to optimize hydraulic safety and efficiency

description: Intervessel pits are considered to function as valves that avoid embolism
 spreading and optimize efficient transport of xylem sap across
 neighbouring vessels. Hydraulic transport between vessels would therefore
 follow a safety-efficiency trade-off, which is directly related to the
 total intervessel pit area (Ap), inversely related to the pit membrane
 thickness (TPM), and driven by a pressure difference. To test this
 hypothesis, we modelled the relative transport rate of gas (ka) and water
 (Q) at the intervessel pit level for 23 angiosperm species, and correlated
 these parameters with the water potential at which 50% of embolism occurs
 (Ψ50). We also measured ka for 10 species using pneumatic measurements.
 The pressure difference across adjacent vessels, and estimated values of
 ka and Q were related to Ψ50, following a convex
 safety-efficiency trade-off based on modelled and experimental data. Minor
 changes in TPM and Ap exponentially affected the pressure difference and
 flow, respectively.  Our results provide clear evidence that a
 xylem safety-efficiency trade-off is not linear, but convex due to flow
 across intervessel pit membranes, which represent mesoporous media within
 microporous conduits. Moreover, the convex nature of long-distance xylem
 transport may contribute to an adjustable fluid balance of plants,
 depending on environmental conditions. 
description: The measured and modelled
 results were processed using R programming (version 4.2.3; R Core Team,
 2023) in RStudio environment (version
 2023.03.0+386)
DOI: 10.57745/ttgglc
title: eco2adapt_Soil SIR_T0_Finland

description: This dataset presents the results of soil SIR (Substrate Induced Respiration) analyses for Finish LL (North Karelia) (Time zero - June 2023)
DOI: 10.57745/uex8ni
title: eco2adapt_Soil SIR_T0_Finland.tab

description: :unav
DOI: 10.5061/dryad.5qfttdzc6
title: SAMC Model Inputs from: Predicting dispersal and conflict risk for wolf recolonization in Colorado

description: The colonization of suitable yet unoccupied habitat due to natural
 dispersal or human introduction can benefit recovery of threatened
 species. Predicting habitat suitability and conflict potential of
 colonization areas can facilitate conservation planning. Planning for
 reintroduction of gray wolves (Canis lupus) to the U.S. state of Colorado
 is underway. Assessing which occupancy sites minimize the likelihood of
 human-wolf conflict during dispersal events and seasonal movements is
 critical to the success of this initiative. We used a spatial absorbing
 Markov chain (SAMC) framework, which extends random walk theory and
 probabilistically accounts for both movement behavior and mortality risk,
 to compare the viability of potential occupancy sites (public lands
 &gt;500 km2 to minimally meet wolf pack range area). The SAMC
 framework produced spatially explicit predictions of wolf dispersal,
 philopatry, and conflict risk ahead of recolonization prior to
 reintroduction efforts. Our SAMC model included: 1) movement resistance
 based on terrain, roads, and housing density; 2) mortality risk and
 potential conflict (absorption) based on livestock presence, social
 tolerance, land ownership, and state boundaries; and 3) site fidelity
 based on habitat quality. Using this model, we compared 21 public land
 units by deriving predictions of: A) relative survival time outside each
 site, B) intensity of use and retention time within each site, and C) the
 probability of use on adjacent public lands. We also predicted and mapped
 potential conflict hotspots associated with each site. Among the units
 assessed, a complex of USFS Wilderness areas near Aspen, chiefly the
 Hunter-Fryingpan and Collegiate Peaks Wilderness areas, had the best
 overall rankings when comparing predictions of each metric. The area
 balances high-quality, well-connected habitat with relatively low
 livestock density and high social tolerance.  Synthesis and
 applications:   Our findings highlight the utility of
 the SAMC framework for assessing colonization areas and the capacity to
 identify locations for effective proactive management, especially of
 conflict-prone species. The flexibility of the SAMC framework enables
 predicting likely areas of philopatry and human-wildlife conflict using
 spatially-explicit metrics which can improve the success of conservation
 translocations and management of species with changing geographic extents.
DOI: 10.34740/kaggle/dsv/14653742
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.cjsxksnc3
title: COI and Cytb data of Lagocephalus spadiceus in eight populations

description: The Late Pleistocene-Holocene climate fluctuations have had a major impact
 on phylogeographic structure and historical dynamics of marine fishes in
 the marginal seas of the western Pacific Ocean. Lagocephalus spadiceus is
 a high-nutritional and economic-value species in the Southeast China Sea.
 The study was to assess the population genetic diversity and demography of
 L. spadiceus in the South China Sea (SCS). A sample of 300 specimens from
 eight geographic locations along the coast of mainland China and Hainan
 Island were obtained for this study. The mitochondrial cytochrome oxidase
 I (COI) and cytochrome b (Cyt b) gene datasets had high haplotype
 diversity but low nucleotide diversity. The genetic structure and
 phylogenetic analyses indicated that there was no significant population
 structure among the eight geographic locations. The low genetic diversity
 of L. spadiceus was associated with population expansion in the Late
 Pleistocene-Holocene period. This was supported by star haplotype
 networks, neutrality tests, unimodal mismatch distributions and Bayesian
 skyline plots. These findings have important reference value for the
 protection of genetic resources. Furthermore, the study illuminates the
 complex relationship between Pleistocene-Holocene temperature variability
 and phylogeography.
description: Forward and reverse splicing of all sequences using SeqMan in
 Larsergene v7.1.0 , and then compare and edit the sequences using the
 Clustal W method in MEGA v7.0 . The <em>COI</em> and Cyt
 <em>b</em> sequences were matched one by one for Multi-locus
 Sequence Analysis (MLSA) using PhyloSuite v1.2.2.
description: Required software: MEGA v7.0 and DnaSP v6.0
description: # Haplotype sequences of mitochondria COI and Cyt b gene datasets ##
 Description of the data and file structure This is the haplotype sequence
 of the mitochondrial COI and CYTB genes of the Lagocephalus spadiceus, can
 be opened with software such as MEGA and DnaSp. COI and CYTB.fas is a
 tandem sequence of COI.fas and CYTB.fas. ## Code/Software MEGA v7.0, DnaSP
 v6.0 , PhyloSuite v1.2.2.
DOI: 10.5061/dryad.98sf7m0q1
title: MERFISH on developing thalamus

description: The thalamus plays a central coordinating role in the brain. Thalamic
 neurons are organized into spatially-distinct nuclei, but the molecular
 architecture of thalamic development is poorly understood, especially in
 humans. To begin to delineate the molecular trajectories of cell fate
 specification and organization in the developing human thalamus, we used
 single-cell and multiplexed spatial transcriptomics. Here we show that
 molecularly-defined thalamic neurons differentiate in the second trimester
 of human development and that these neurons organize into spatially and
 molecularly distinct nuclei. We identify major subtypes of glutamatergic
 neuron subtypes that are differentially enriched in anatomically distinct
 nuclei. In addition, we identify six subtypes of GABAergic neurons that
 are shared and distinct across thalamic nuclei.
DOI: 10.5061/dryad.h44j0zprt
title: Raw target enrichment of conserved element sequence data for 24 black coral species

description: Deep-sea lineages are generally thought to arise from shallow-water
 ancestors, but this hypothesis is based on a relatively small number of
 taxonomic groups. Anthozoans, which include corals and sea anemones, are
 significant contributors to the faunal diversity of the deep sea, but the
 timing and mechanisms of their invasion into this biome remain elusive.
 Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83
 species in the order Antipatharia (black coral) to investigate their
 bathymetric evolutionary history. Our reconstruction indicates that extant
 black coral lineages first diversified in continental slope depths
 (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently
 radiated into, and diversified within, both continental shelf (&lt;250
 m) and abyssal (&gt;3,000 m) habitats. Ancestral state reconstruction
 analysis suggests that the appearance of morphological features that
 enhanced the ability of black corals to acquire nutrients coincided with
 their invasion of novel depths. Our findings have important conservation
 implications for anthozoan lineages, as the loss of “source” slope
 lineages could threaten millions of years of evolutionary history and
 confound future invasion events, thereby warranting protection.
description: DNA was extracted using a Qiagen Puregene Tissue Kit using the
 DNA Purification from Tissue protocol. PCR inhibitors were removed from
 DNA using a Qiagen DNeasy PowerClean Clean Up Kit. A Qubit 2.0 fluorometer
 was used to measure the initial concentration of each extracted DNA sample
 and then the DNA was precipitated out, dried down and sent to Arbor
 Biosciences (Ann Arbor, MI) for library preparation, hybrid enrichment and
 sequencing, following details in Quattrini et al. The targeted enrichment
 of UCE and exonic loci was carried out using the hexacoral-v2 probe
 design, which includes 25,514 baits targeting 2,499 loci. Bioinformatic
 post-sequencing analyses were conducted following the Phyluce online
 documentation (https://phyluce.readthedocs.io/en/latest/tutorial-one.html), including raw read trim and matching of loci to UCE and exon probes. SPAdes v3.12.0 was used outside of the phyluce pipeline to assemble trimmed raw reads using the main executable script spades.py and a coverage cutoff of 2. Individually aligned UCE/exon loci were filtered to include only those that were present in at least 50% of the samples. All code used in this study is detailed in Dataset S1.
description: Phyluce and SPAdes v3.12.0.
DOI: 10.5061/dryad.dz08kps3f
title: Bees exposed to climate change are more sensitive to pesticides

description: Bee populations are exposed to multiple stressors, including land-use
 change, biological invasions, climate change and pesticide exposure, that
 may interact synergistically. We analyze the combined effects of climate
 warming and sublethal insecticide exposure in the solitary bee Osmia
 cornuta. Previous Osmia studies show that warm wintering temperatures
 cause body weight loss, lipid consumption and fat body depletion. Because
 the fat body plays a key role in xenobiotic detoxification, we expected
 that bees exposed to climate warming scenarios would be more sensitive to
 pesticides. We exposed O. cornuta females to three wintering
 treatments: current scenario (2007-2012 temperatures), near-future
 (2021-2050 projected temperatures), and distant-future (2051-2080). Upon
 emergence in spring, bees were orally exposed to three sublethal doses of
 an insecticide (Closer, a.i. sulfoxaflor; 0, 4.55 and 11.64 ng a.i./bee).
 We measured the combined effects of wintering and insecticide exposure on
 phototactic response, syrup consumption, and longevity. Wintering
 treatment by itself did not affect winter mortality, but body weight loss
 increased with increasing wintering temperatures. Similarly, wintering
 treatment by itself hardly influenced phototactic response or syrup
 consumption. However, bees wintered at the warmest temperatures had
 shorter longevity, a strong fecundity predictor in Osmia. Insecticide
 exposure, especially at the high dose, impaired the ability of bees to
 respond to light, and resulted in reduced syrup consumption and longevity.
 The combination of the warmest winter and the high insecticide dose
 resulted in a 70% longevity decrease. Smaller bees, resulting from smaller
 pollen-nectar provisions, had shorter longevity suggesting nutritional
 stress may further compromise fecundity in O. cornuta. Our results show a
 synergistic interaction between two major drivers of bee declines, and
 indicate that bees will become more sensitive to pesticides under the
 current global warming scenario. Our findings have important implications
 for pesticide regulation and underscore the need to consider multiple
 stressors to understand bee declines.
DOI: 10.5061/dryad.sqv9s4n8r
title: Data from: Community Credit survey on trust in consumer financial services

description: The Community Credit research project explores pathways for trusted
 collaboration between credit unions and the communities they serve. To
 understand the experiences of people historically underserved by the
 consumer financial services industry, we focused in particular on the
 lived experience of low-income residents in Southern California. As part
 of a larger, mixed-methods study, in 2022 we conducted an online survey
 investigating people’s everyday financial practices, evolving perceptions
 of trust and risk, and their unmet financial needs. The general population
 survey data was collected between April 15 and April 22, 2022. The credit
 union data was collected between May 3 and July 18, 2022. This data set
 contains the responses of the survey participants after excluding any
 personally identifying data. All study materials and procedures were
 approved by the University of California, Irvine Office of Human Research
 Protections and the Institutional Review Board (protocol ID 20216839).
 This material is based upon work supported by the National Science
 Foundation under Grant No. 2137567. Any opinions, findings, and
 conclusions or recommendations expressed in this material are those of the
 author(s) and do not necessarily reflect the views of the National Science
 Foundation.
description: Survey data was collected via the
 Qualtrics platform. The survey contains 52 questions. It was distributed
 to the general population in zip codes within the counties of Los Angeles
 and Orange. It was also distributed directly to members of a large credit
 union headquartered in Orange County (“large” according to NCUA asset
 classes). Participants were eligible to complete the survey if they live
 in Orange County or Los Angeles County, are older than 18, and have a
 combined household income of less than $100,000. Incomplete responses have
 been removed. The survey yielded 1,370 complete responses (1,213 from the
 general population participants and 157 from members of the large credit
 union).
description: Note that the files do not contain
 all the responses from the survey questions. Responses that provided
 potentially identifying information were removed. Survey participants’
 gender, education status, employment status, and marital status were
 removed; data on these elements are provided in aggregate in the readme
 file. Responses are segmented into two files reflecting participants from
 the general population (“Gen Pop”) and from the credit union
 (“CU”).
DOI: 10.5061/dryad.c59zw3rdz
title: Predation affects body shape in the knife livebearer Alfaro cultratus (Cyprinodontiformes: Poeciliidae)

description: Livebearing fishes are a common model for studying the effect of predation
 on prey biology. Numerous studies have found differences in life history,
 sexual selection, behavior, and morphology between populations of the same
 species that co-occur with predators and those that do not. Alfaro
 cultratus is a livebearing fish with populations in different predation
 environments, but unlike other livebearers, this species also has an
 extreme body shape that is laterally compressed. Given this unusual
 morphology, we asked if predation environment would still predict overall
 body shape, as has been documented in other species. We collected
 specimens from both predator and no-predator sites in Costa Rica and used
 a geometric morphometrics analysis to determine if body shape is affected
 by predation environment while controlling for size and river gradient.
 Body shape does indeed differ between predation environments; however, the
 observed differences contrast with the patterns found in other livebearer
 systems. Alfaro cultratus in predation environments had deeper and shorter
 bodies and deeper caudal peduncles than those found in environments
 without dominant fish predators.
description: We used 459 female specimens of <em>Alfaro</em>
 <em>cultratus</em> for our analysis. We photographed all
 specimens on their left side and digitized 11 landmarks to characterize
 body shape (Figure 2), using the software tpsDig.  The
 predictor variable files list every specimen in the dataset with a column
 for its location ID, Gradient, High or Low Predation environment, Museum
 number ID, Centroid size and Order ID. This file is necessary for the
 multivariate linear mixed model.
description: ## Predation affects body shape in the knife livebearer Alfaro cultratus
 (Cyprinodontiformes: Poeciliidae) ## Description of the data and file
 structure TPS file: First line states the number of landmarks used, the
 next eleven lines show values for X and Y for each landmark. This is then
 followed by the corresponding image file name, the ID for the order of
 specimens and the scale value from the Generalized Procrustes Analysis.
 This is then repeated for each of the 459 specimens. Text document: This
 file has one line for each of the 459 specimens. The first column shows at
 which locality was the specimen collected, the second shows a gradient
 value for that site, the third column indicates whether this is a low (0)
 or high predation (1) site, the fourth line is a unique museum ID for the
 BYU Life History Museum, the fifth line is the centroid size value
 calculated from the landmark positions and the final column is an order ID
 which matches the ID to each specimen's landmark data on the TPS
 file.
DOI: 10.15468/dl.wb3h3q
title: Occurrence Download

description: A dataset listing the 205 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Aves del Parque Nacional Cumbres de Monterrey, Nuevo León, México"
 ]
}

 The dataset's 205 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003578-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tmpg4f54n
title: Supplemental material for the insight: High levels of mercury contamination in a necrophage dung-beetle of the Amazon rainforest (Scarabaeidae: Scarabaeinae)

description: This study represents the first evidence of mercury contamination in the
 family Scarabaeidae, with a close focus to Coprophanaeus lancifer, the
 largest copro-necrophagous beetle in South America. This work shows the
 repartition of total mercury (THg) in the insect body and lays the
 groundwork for additional future studies.
description: These datasets were collected at Los Amigos Biological Station
 and Finca Las Piedras, two Biological Stations in the Madre de Dios region
 of Peru (2022).
description: Microsoft Excel is needed to open file "Hg_Analyses -
 Final_Results CINCIA (July 2022).xlsx" Missing
 values are denoted by n/a. Additional details are available in the README
 file.
DOI: 10.82294/dvnj5mqcw
title: Replication Data for: Citas testimoniales: Procesos interdisciplinares. Territorio: Todos. Sector: Todos. Año: 2023

description: Esta agrupación de códigos está diseñada para identificar cómo los educadores integran diferentes saberes en su práctica, de qué forma invitan a otros educadores, sabedores y artísticas a involucrarse de manera operativa y de manera conceptual o de diseño en sus espacios educativos, por lo que estos códigos develan qué prácticas, saberes y conocimiento por fuera de su base formativa han podido integrar a sus clases.
DOI: 10.5061/dryad.4f4qrfjjc
title: Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA

description: Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain
 population-level data due to either a lack of taxonomic resolution for the
 molecular method used, limitations in the reference material or
 inefficient methods. Here, we present the potential of multiplexing
 different PCR primers to retrieve population-level genetic data from
 sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species
 with a circumpolar distribution and three lineages for present-day
 populations. We searched 18 plastid genomes for intraspecific variable
 regions and developed 61 primers to target these. Initial multiplex PCR
 testing resulted in a final set of 38 primers. These primers were used to
 analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present)
 from five different localities in northern Norway, the Alps and the Polar
 Urals. All known V. uliginosum lineages in these regions and all primers
 could be recovered from the sedaDNA data, where for each sample
 28.1 primers containing 34.15 variant sequences were obtained on average.
 All sediment samples were dominated by a single lineage, except three
 alpine samples which had co-occurrence of two different lineages.
 Furthermore, lineage turnover was observed in the Alps and northern
 Norway, suggesting that present-day phylogeographical studies may overlook
 past genetic patterns. Multiplexing primers is a promising tool for
 generating population-level genetic information from sedaDNA. The
 relatively simple method, combined with high sensitivity, provides a
 scalable method that will allow researchers to track populations through
 time and space using environmental DNA.
description: DNA was extracted from 20 sediment samples and 4
 extraction/sampling negative controls using a modified DNeasy PowerSoil
 kit (Qiagen, Germany) protocol in the ancient DNA laboratory at TMU. DNA
 extracts and negative extraction/sampling controls were amplified with a
 dual-tagged multiplex primer sets that amplified 38 intraspecific regions
 on the <em>Vaccinium uliginosum </em>chloroplast.
 The OBITools software package was used for the bioinformatics
 pipeline. Paired-end reads were aligned using SeqPrep (https://github.com/jstjohn/SeqPrep/releases, v1.2). Merged reads were demultiplexed according to the 4 bp primer tags and identical sequences were collapsed. Singleton sequences and those shorter than 10 bp were removed and putative artifactual sequences were identified and removed from the dataset. The multiplex marker data was identified with a reference dataset.
description: The data files are "Tab-Separated Values" (TSV) files
 and can be opened with any text editor, imported into spreadsheet
 software, analysed with stastical programs such as R, parsed with command
 line tools or scripting languages. The Python script
 can be ran from the command line. The fasta files are
 plain text and can be opened in any text editor.