cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h18931zr0
title: Data for: Exploitation competition between seed predators and dispersers introduced to Hawaiian forests

description: Exploitation competition occurs when one group of organisms reduces the
 availability of a resource for another group of organisms. For instance,
 plants produce a certain number of fruits for seed dispersal by
 fruit-eating animals (hereafter frugivores), and fruit consumption by one
 group of frugivores can reduce the number of fruits available for other
 frugivores. However, it is uncertain whether exploitation competition is
 common among frugivores, particularly in novel ecosystems, where food
 resources are generally thought to be abundant and invasive species are
 dietary generalists. In a novel ecosystem in Hawai‘i, we used gut passage
 experiments with captive birds to identify roles of introduced frugivores
 and found they were either distinctly seed dispersers or predators. We
 then experimentally tested how frugivory by seed predators influenced
 frugivory by seed dispersers. Specifically, we used exclosures around
 fruiting plants that blocked seed predator access, while permitting seed
 disperser access, and we had two control treatments that allowed for
 access by all frugivores (n=139 plants). When seed predators were excluded
 from plants, there was more frugivory by dispersers compared to controls,
 and results varied by year and plant species. Overall, we show that
 introduced frugivores occupied distinct ecological roles (seed predator or
 seed disperser), exploitation competition occurred between these
 introduced frugivore groups, and seed predators had both direct (via seed
 destruction) and indirect (via reduction in frugivory by dispersers)
 effects on seed dispersal. Thus, in this novel ecosystem, multiple
 frugivory is subtractive, and competition for fruit between introduced
 seed predators and seed dispersers scales up to affect invasions and the
 conservation of native flora.
DOI: 10.7910/dvn/73l5ix
title: Replication Data for: Beyond Hate Speech: Online Rumors and Out-Group Resentment in Divided Societies

description: The political consequences of hate speech on social media are the subject of intense research. Studies from Europe and North America have found that online exposure to hate speech affects both attitudes and offline behavior. Moving beyond hate speech, we show how little it takes for online rumors to stoke inter-group tensions in divided societies. In a pre-registered survey experiment with 3,075 Hindu social media users in India, we navigate ethical challenges with very mild information treatments, post-treatment fact-checks, and debriefs. We find that even subtle online rumors change sentiments toward entire groups and heighten conflict-related emotions, especially when combined with injustice frames. As none of our information treatments classify as hate speech, these problems appear inherent to social media technology and point toward a need for a broader debate on policy responses.
DOI: 10.5061/dryad.dr7sqvb2z
title: Dairy farmer semi-structured interview responses related to bald eagles (Haliaeetus leucocephalus) in Washington state

description: This data provides responses to semi-structured interviews conducted with
 dairy farmers in Whatcom County, Washington State, USA. The goal of the
 interviews were to gather information on eagle activity in agricultural
 and dairy settings, and to assess farmers relationships with bald eagles
 on their farms. 
description: Our questionnaire contained 12 core questions related to eagle
 abundance, behavior, phenology, and the perception of eagles by farmers.
 Interviews began with an explanation that this was an independent research
 project by university students, with no affiliation with government
 agencies, and that all answers would be treated anonymously. We
 prioritized speaking with dairy farm owners but would interview employees
 if designated by the owner. Out of the 78 dairy farms in Whatcom County,
 27 were approached for an interview. These farms were chosen based on
 proximity to previously conducted eagle–farm surveys in Whatcom County
 (Figure 1 in Duvall 2022). Twenty farmers were willing to be interviewed,
 representing 74% of farms approached, and 25.6% of all the dairy farms in
 Whatcom County. Two interviewers were present for each interview: one to
 lead questions, and one to record responses. These responses were later
 transffered into a spreadsheet which is presented here.
DOI: 10.5061/dryad.fj6q573zv
title: Large carnivore conservation and traditional pastoralism: An economic analysis on the efficacy of bear-reindeer predation mitigation measures: Dataset for 2014–2016 corralling versus forest treatment analysis

description: While wildlife and cultural preservation goals can be either complimentary
 or counteractive, the goals of large carnivore conservation and
 traditional pastoralist lifestyles are often at odds.  Livestock
 depredation can negatively impact the economies of livestock herders,
 while subsequent lethal removals contribute to local carnivore population
 declines. Here, we collaborated with two Sámi reindeer herding communities
 (2010–2016) situated in Sweden’s boreal forest to evaluate the efficacy
 and economic feasibility of three brown bear predation mitigation
 measures: corralling pregnant reindeer during parturition, lethal bear
 management removals, and public bear-license hunting. Calving corrals
 increased survival for reindeer calves born to average-sized females by 7%
 to 15% and by 14% to 30% for calves born to small females. However, the
 realized cost of implementing calving corrals outweighed the financial
 gain for both our study areas (net losses ranged between €1,111 and €6,210
 per calf saved from bear predation per year when using the updated 2021
 calf value), as well as for almost every theoretical scenario we explored
 (net losses €234 and €13,995 per calf saved from bear predation). The
 exception was the theoretical scenario where small herding communities
 overlapped large bear populations, which crossed the breakeven efficacy
 bear/reindeer ratio of 13.5 bears/100 reindeer and had a potential net
 gain of €36 per saved calf. Similarly, the cost of lethal management
 removals of bears also outweighed the potential financial gain from saved
 calves, with net losses between €75 and €239 per calf. License hunting,
 where the hunters voluntarily incur the monetary costs of removing bears,
 is in most cases the only economically viable mitigation measure where the
 cost of mitigation did not outweigh the financial gain from increased
 reindeer survival. While the annual public license hunt was the most
 cost-effective mitigation measure, it may be less biologically effective,
 i.e., bear hunting occurs in the fall and reindeer parturition the
 following spring which leaves time for the empty niche of harvested bears
 to be filled by survivors. Economically and biologically effective
 predation mitigation measures are key for promoting coexistence, and we
 suggest that potential mitigation measures should be studied in
 collaboration with local people.
DOI: 10.5061/dryad.7h44j0zzd
title: Parasite detection and quantification in avian blood is dependent on storage medium and duration

description: Studies of parasites in wild animal populations often rely on molecular
 methods to both detect and quantify infections. However, method accuracy
 is likely to be influenced by the sampling approach taken prior to nucleic
 acid extraction. Avian Haemosporidia are studied primarily through the
 screening of host blood, and a range of storage mediums are available for
 the short- to long-term preservation of samples. Previous research has
 suggested that storage medium choice may impact the accuracy of PCR-based
 parasite detection, however, this relationship has never been explicitly
 tested and may be exacerbated by the duration of sample storage. These
 considerations could also be especially critical for sensitive molecular
 methods used to quantify infection (qPCR). To test the effect of storage
 medium and duration on Plasmodium detection and quantification, we split
 blood samples collected from wild birds across three medium types (filter
 paper, Queen’s lysis buffer, and 96% ethanol) and carried out DNA
 extractions at five time-points (1, 6, 12, 24 and 36 months
 post-sampling). First, we found variation in DNA yield obtained from blood
 samples dependent on storage medium which had subsequent negative impacts
 on both detection and estimates of Plasmodium copy number. Second, we
 found that detection accuracy (incidence of true-positives) was highest
 for filter paper stored samples (97%), while accuracy for ethanol and
 Queen’s lysis buffer-stored samples was influenced by either storage
 duration or extraction yield respectively. Lastly, longer storage
 durations were associated with decreased copy number estimates across all
 storage mediums; equating a 58% reduction between the first- and
 third-year post-sampling for lysis-stored samples. These results raise
 questions regarding the utility of standardising samples by dilution,
 while also illustrating the critical importance of considering storage
 approaches in studies of Haemosporidia comparing samples subjected to
 different storage regimes and/or stored for varying lengths of time.
DOI: 10.6078/d17416
title: Data for: Re-collected after 55 years: a new species of Bembidion (Coleoptera, Carabidae) from California

description: A new species of the carabid beetle genus Bembidion Latreille is described
 from the Central Valley, Los Angeles Basin, and surrounding areas of
 California. Bembidion brownorum sp. nov. is a distinctive
 species, a relatively large member of subgenus Notaphus Dejean, and within
 Notaphus, a member of the Bembidion obtusangulum LeConte species
 group.  It has faint spots on the elytra and a large, convex,
 rounded prothorax. Of the 22 specimens from 11 localities, all but one
 were collected more than 55 years ago. Although the collection of the
 holotype in 2021 at UV light suggests the species is still extant, the
 lack of other recent specimens suggests the species may have a more
 restricted distribution than in the past, and its populations may be in
 decline.
description: DNA was extracted using a Qiagen DNeasy Blood and Tissue Kit.
 Fragments for the four genes were amplified using the Polymerase Chain
 Reaction on an Eppendorf Mastercycler Pro Thermal Cycler, using TaKaRa Ex
 Taq and the basic protocols recommended by the manufacturers.
 Assembly of multiple chromatograms for each gene fragment and
 initial base calls were made with Phred (Green and Ewing 2002) and Phrap
 (Green 1999) as orchestrated by Mesquite's Chromaseq package
 (Maddison and Maddison 2021a; Maddison and Maddison 2021c), with
 subsequent modifications by Chromaseq and manual inspection. Multiple
 peaks at a single position in multiple reads were coded using IUPAC
 ambiguity codes.    Maximum likelihood analysis was
 conducted for each gene individually using IQ-TREE and trees from standard
 bootstrap analysis in IQ-TREE of the concatenated matrix.
description: This file, intended to be opened in Mesquite (http://www.mesquiteproject.org) contains 4 single-gene matrices as well as a concatenated matrix.
DOI: 10.5281/zenodo.18305164
title: Persistent high PM pollution in the Eastern Mediterranean and Middle East: Insights from long-term observations and source apportionment in Cyprus

description: Long-term PM2.5 and PM10 chemical composition data (in μg/m3)  at un urban traffic (NICTRA) and regional background  (AMX) sites in Cyprus
DOI: 10.5281/zenodo.18305165
title: Persistent high PM pollution in the Eastern Mediterranean and Middle East: Insights from long-term observations and source apportionment in Cyprus

description: Long-term PM2.5 and PM10 chemical composition data (in μg/m3)  at un urban traffic (NICTRA) and regional background  (AMX) sites in Cyprus
DOI: 10.5061/dryad.2jm63xsth
title: Species, hybrid and genotype effects on leaf litter curling, and their extended consequences for spiders and soil moisture dynamics

description: This archive contains datasets from a group of studies testing the
 hypotheses that leaf litter curling is influenced by plant species,
 hybridization and genotype, and has extended consequences for associated
 organisms and soil processes. A novel litter curling index (LCI) was used
 to characterize the curling of newly senesced leaves. There are four
 distinct datasets represented here. 1) A dataset of LCI from 11 plant
 species (tall annual forb = Helianthus annuus L.; evergreen shrubs =
 Arctostaphylos pungens Kunth, Quercus turbinella Greene, Rhus ovata S.
 Watson; deciduous shrubs = Rhus trilobata Nutt., Ribes cereum Douglas,
 Acer glabrum Torr.; deciduous trees = Elaeagnus angustifolia L., Quercus
 gambelii Nutt., Populus tremuloides Michx., Populus fremontii S. Watson)
 mostly growing in natural habitats of Northern Arizona, USA. 2) A dataset
 containing LCI from two Populus species (P. fremontii James, P.
 angustifolia S. Watson) and their F1 hyrbids in a common garden
 in Ogden, UT, USA  (including replicated genotypes of P.
 angustifolia but not the other tree types). 3) The third dataset examined
 the relationship between average LCI for a tree and the abundance of
 agilenid webs under Populus trees growing in a common garden; the LCI
 values are averages per tree from data collected for dataset 2, and
 previously published spider web data. 4) The last dataset contains litter
 and soil moisture values from a litter/soil drying experiment that tested
 the effect of litter curling on soil moisture dynamics. See the README
 file for more details on the different datasets.
description: The new method, termed LCI for litter curling index, is derived
 by dividing the surface area of a scanned image of a dried curled leaf
 (LC) by the surface area of a fully flattened image (LF) of the same
 individual piece of litter (LC/LF). The ratio of curled to flattened
 litter surface area is then subtracted from 1 (i.e., 1 – (LC/LF)) to
 create an LCI value that theoretically ranges from 0 to nearly 1, where
 increasing LCI scores equate to increasing deviation from flatness (i.e.,
 more curled). LCI was measured on a total of 1,757 individual freshly
 senesced leaves from 176 individual plants, representing 12 species and
 one hybrid taxon. Spider webs were measured as in Wojtowicz et al.
 (2014; DOI 10.1007/s00442-014-2998-3). The litter curling experiment was
 done using leaf litter placed on the surface of pots, watering the pots,
 then measuring soil and litter moisture over the course of several weeks.
 The four litter treatments in the drying experiment were naturally flat
 <em>Populus fremontii</em>, experimental control <em>P.
 fremontii </em>(naturally flat leaf with a paper clip),
 experimentally curled <em>P. fremontii</em> (experimentally
 curled and held with a paper clip), and naturally curled <em>P.
 angustifolia</em>.
description: All you need is microsoft excel or an equivalent spreadsheet
 program.
DOI: 10.5061/dryad.9ghx3ffn8
title: Data for: Vertebrate digging alters plants and soils

description: Soil-disturbing animals are common globally and play important roles in
 creating and maintaining healthy functional soils and landscapes. Yet many
 of these animals are threatened or locally extinct, either by habitat
 loss, predation by non-native animals or poaching/poisoning. Some
 reintroduction and rewilding programs have as their core aims both the
 increase in animal populations and reinstatement of processes that have
 been lost due to their extirpation. Here we review the effects of
 soil-disturbing vertebrates on ecosystem processes, using a
 meta-analytical approach to advance the argument that they can be used to
 rehabilitate degraded ecosystems, by altering mainly composition and
 function, but with fewer positive effects on structure. We describe four
 case studies showing that loss or reintroduction of soil-disturbing
 vertebrates leads to ecosystem state changes, and highlight the role of
 spatial scale, co-varying management changes, and species co-occurrence in
 modulating their effects. We discuss the advantages and disadvantages of
 using soil-disturbing vertebrates over mechanised engineering approaches
 such as pitting and furrowing, including more self-sustainable and
 heterogenous disturbances, creation of new habitats, and added
 recreational values. Finally, we identify key knowledge gaps in our
 understanding of the use of soil-disturbing vertebrates for rehabilitating
 degraded ecosystems.
description: We used the global database of Mallen-Cooper et al. (2019) and
 updated it with papers published up until September 2022 that contained
 information on soil disturbance by vertebrates published between November
 2016 and September 2022. We maintained the same search string used by
 Mallee-Cooper et al. (2019) and used the ISI Web of Knowledge and Google
 Scholar: biopedturbation, biopedoturbation, faunalpedoturbation,
 faunalturbation, “foraging pits” and zoogeomorphology. Studies were
 restricted to terrestrial environments and where a publication reported
 data on the effects of vertebrates on plants, soils, or ecological
 processes, and compared this with a paired undisturbed control. Our
 searching resulted in a combined database of 2437 records for 70
 vertebrate species across all continents except Antarctica (Fig. 1a). In
 total we had data on 35 attributes (electronic supplementary material,
 table S2), including four that were unclassified (lizard size, cover of
 micro-depressions, rock cover and proportion of exotic plants,
 representing 102 records). From these studies we extracted the raw means
 and variances of the different attributes. We used ImageJ to extract data
 from figures.
description: No specific packages, only Microsoft Excel to calculate means and
 confidence intervals.
DOI: 10.5061/dryad.f1vhhmh1p
title: MinION sequencing data of mtDNA from BH10 cells

description: Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic
 because of its uniparental inheritance and subsequent homoplasmic state,
 which excludes the biological need for genetic recombination, as well as
 limits tools to study it. However, molecular recombination is an important
 genome maintenance mechanism for all organisms, most notably being
 required for double-strand break repair. To demonstrate the existence of
 mtDNA recombination, we have taken advantage of a cell model with two
 different types of mitochondrial genomes and impaired ability to turn over
 broken mtDNA. The resulting excess of linear DNA fragments caused
 increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA
 complexes and recombinant mtDNA genomes, detectable by Southern blot.
 Combining our observations with previously published work, we propose that
 the mitochondrial replisome can catalyze microhomology-mediated
 recombination of linear mtDNA ends, thus rendering a specialized
 mitochondrial recombinase unnecessary. The error-proneness of this system
 is likely to contribute to the formation of pathological mtDNA
 rearrangements.
description: The data consists of original FASTQ files of nanopore sequencing
 data.  Mitochondrial DNA was linearised through the
 digestion of isolated mitochondrial with <em>BamHI</em> at
 37°C for 2 h. Size selection was done using AMPure XP beads with a
 bead-to-volume ratio of 0.8. Nanopore sequencing was performed in
 accordance with the Native barcoding genomic DNA protocol with EXP-NBD104,
 EXP-NBD114 and SQK-LSK109 (version
 NBE_9Q65_V109_revAE_14Aug2019). The end processing was done according to the
 manufacturer’s instructions using NEBNext FFPE DNA Repair Mix and NEBNext
 Ultra II End repair/dA-tailing Module reagents. Barcode labelling was done
 with Native Barcoding Expansion 1-12 and NEB Blunt/TA Ligase Master Mix
 (M0367). Nanopore
 sequencing libraries were then prepared using 100 ng of linear mtDNA
 following the protocol of the ligation sequencing kit (Oxford Nanopore
 Technologies item number: SQK-LSK109). Adapter ligation was done with NEBNext Quick
 Ligation Reaction Buffer (NEB B6058), Adapter Mix II (AMII), and Quick T4
 DNA ligase. The Nanopore
 sequencing libraries were then sequenced on the Oxford Nanopore Flongle
 device, using Flongle
 Sequencing Expansion (EXP-FSE001) and Flush Tether. Basecalling of the Nanopore sequencing was
 performed on the CSC Puhti system using Guppy v.
 5.0.7.
DOI: 10.5061/dryad.zw3r228c4
title: RNA polymerase evolution FASTQ files (2/2)

description: RNA polymerase (RNAP) is emblematic of complex biological systems that
 control multiple traits involving trade-offs such as growth versus
 maintenance. Laboratory evolution has revealed that mutations in RNAP
 subunits, including RpoB, are frequently selected. However, we lack a
 systems view of how mutations alter the RNAP molecular functions to
 promote adaptation. We, therefore, measured the fitness of thousands of
 rpoB variants under multiple conditions and genetic backgrounds,
 to find that adaptive mutations cluster in two separate modules. Mutations
 in one module favor growth over maintenance through a partial loss of an
 interaction associated with faster elongation. Mutations in the other
 favor maintenance over growth through a destabilized RNAP-DNA complex. The
 two molecular handles capture the versatile RNAP-mediated
 adaptations. Combining both interaction losses simultaneously improved
 maintenance and growth, challenging the idea that growth-maintenance
 tradeoff resorts only from limited resources, and revealing how
 compensatory evolution operates within RNAP.
description: # Title of Dataset *** The dataset is linked to the above article. Here we
 have uploaded the sequencing data. The code and processed data can be
 found in linked Dryad: DOI: 10.5061/dryad.n8pk0p30n ## Description of the
 data and file structure The information about the fastq data and the
 associated samples from which they were extracted can be found in the tsv
 file: Sample checklist\_1674571220193.tsv. Details on the file
 experimental sample map can be found in the tsv file:
 fastq2\_template\_1674570722019.tsv. The files are in the dryad
 submission: 10.5061/dryad.n8pk0p30n See that submission for more details
 on this data. ## Code/Software The detailed code can be found
 at:https://github.com/Alaksh/RNA-Polymerase-Evolution.git and Zenodo link:
 10.5281/zenodo.8144064
DOI: 10.5281/zenodo.18402880
title: Xojiyev Shohruh Saidjappar o'g'li, & Worldly Knowledge Publishing Centre. (2026). RAQAMLI TEXNOLOGIYALAR ASOSIDA MASHG'ULOT JARAYONINI REJALASHTIRISH [Data set]. В ILM FAN XABARNOMASI (Т. 11, Выпуск 02, сс. 2444–2452). Zenodo. https://doi.org/10.5281/zenodo.18402846

description: Ekologiya sohasiga oid atamalar hozirgi kunda atrof-muhit bilan bog‘liq muammolarga yechim izlashda tayanch vazifani bajaradi. Ekologik atamalarni nafaqat tilshunoslik, balki tarjimashunoslik sohalarida ham chuqur o‘rganish mumkin. Ushbu maqolada ekologik terminlar haqida umumiy ma’lumot va ular qo‘llaniladigan sohalar batafsil va misollar bilan yoritiladi.
DOI: 10.5281/zenodo.18402881
title: Xojiyev Shohruh Saidjappar o'g'li, & Worldly Knowledge Publishing Centre. (2026). RAQAMLI TEXNOLOGIYALAR ASOSIDA MASHG'ULOT JARAYONINI REJALASHTIRISH [Data set]. В ILM FAN XABARNOMASI (Т. 11, Выпуск 02, сс. 2444–2452). Zenodo. https://doi.org/10.5281/zenodo.18402846

description: Ekologiya sohasiga oid atamalar hozirgi kunda atrof-muhit bilan bog‘liq muammolarga yechim izlashda tayanch vazifani bajaradi. Ekologik atamalarni nafaqat tilshunoslik, balki tarjimashunoslik sohalarida ham chuqur o‘rganish mumkin. Ushbu maqolada ekologik terminlar haqida umumiy ma’lumot va ular qo‘llaniladigan sohalar batafsil va misollar bilan yoritiladi.