cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q573n5tkz
title: A new titanopteran Magnatitan jongheoni gen. et sp. nov. from southwestern Korean Peninsula

description: Titanopterans are spectacular giant predatory insects mainly known from
 the Triassic, but they are known from a few localities in Central Asia
 (including European Russia) and Australia. The Nampo Group is a non-marine
 sequence, located at the southwest Korean Peninsula, the age of which has
 remained controversial, due to lack of proper age-constraining fossils.
 Here we report a new titanopteran Magnatitan jongheoni gen. et
 sp. nov. from the Amisan Formation, the Nampo Group. The division of RA
 and RP beyond the distal half of the fossil wing is a characteristic of
 the family Paratitanidae. This is the first discovery of a titanopteran
 fossil outside Central Asia and Australia, suggesting a possible
 circum-Tethys Ocean distribution. Given the possibly widespread
 distribution of titanopterans, this group may have played a critical role
 as giant predatory insects in the Triassic terrestrial ecology. Since
 titanopterans have never been found beyond the Triassic-Jurassic boundary,
 the occurrence of a titanopteran corroborates the Triassic age of the
 Nampo Group.
description: 50 images were taken and
 converted into a PTM format file which was then run in RTI Viewer software
 which is freely downloadable at http://culturalheritageimaging.org/What_We_Offer/Downloads/.
DOI: 10.5061/dryad.xgxd254jb
title: Population genomics of an Octopus species identify oceanographic barriers and inbreeding patterns: Demultiplexed reads of 71 Octopus insularis individuals

description: Coastal marine ecosystems are highly productive and important for global
 fisheries. To mitigate over-exploitation and to establish efficient
 conservation management plans for species of economic interest, it is
 necessary to identify the oceanographic barriers that condition divergence
 and gene flow between populations with those species, and that determine
 their relative amounts of genetic variability. Here, we present the first
 population genomic study of an Octopus species, Octopus insularis, which
 was described in 2008 and is distributed in coastal and oceanic island
 habitats in the tropical Atlantic Ocean, Gulf of Mexico and the Caribbean
 Sea. Using genomic data, we identify the South Equatorial current as the
 main barrier to gene flow between southern and northern parts of the
 range, followed by discontinuities in the habitat associated with depth.
 We find that genetic diversity of insular populations significantly
 decreases after colonization from the continental shelf, also reflecting
 low habitat availability. Using demographic modelling, we find signatures
 of a stronger population expansion for coastal relative to insular
 populations, consistent with estimated increases in habitat availability
 since the Last Glacial Maximum. The direction of gene flow is coincident
 with unidirectional currents and bidirectional eddies between otherwise
 isolated populations. Together, our results show that oceanic currents and
 habitat breaks are determinant in the diversification of coastal marine
 species where adults have a sedentary behavior but paralarvae are
 dispersed passively, shaping standing genetic variability within
 populations. Lower genetic diversity within insular populations implies
 that these are particularly vulnerable to current human exploitation and
 selective pressures, calling for the revision of their protection status.
description: single-end ddRAD-seq data demultiplexed with ipyrad v.0.9.50
description: # Population genomics of an Octopus species identify oceanographic
 barriers and inbreeding patterns: Demultiplexed reads of 71 Octopus
 insularis individuals
 [https://doi.org/10.5061/dryad.xgxd254jb](https://doi.org/10.5061/dryad.xgxd254jb) This repository contains the demultiplexed raw reads of 71 *Octopus insularis* individuals created with single-end ddRAD sequencing. ## Description of the data and file structure Details can be found in our article in Marine Biology: Population genomics of an Octopus species identify oceanographic barriers and inbreeding patterns, or in our preprint: [10.22541/au.164672071.18620221/v1](https://doi.org/10.22541/au.164672071.18620221/v1) ## Sharing/Access information This is the primary source for the data. ## Code/Software Scripts used to analyse the data are available here: https://github.com/casparbein/OctopusInsularis
DOI: 10.5281/zenodo.17662344
title: Database experimental data "Two-phase hydrodynamics and aerosol mass transfer characterization in pool scrubbing: a simultaneous measurement technique"

description: ## DATABASE EXPERIMENTAL DATA "TWO-PHASE HYDRODYNAMICS AND AEROSOL MASS TRANSFER CHARACTERIZATION IN POOL SCRUBBING: A SIMULTANEOUS MEASUREMENT TECHNIQUE"Reference Open-Access journal publication: Alvaro Ramos Perez, Terttaliisa Lind, Victor Petrov, Annalisa Manera, Horst-Michael Prasser,Two-phase hydrodynamics and aerosol mass transfer characterization in pool scrubbing: A simultaneous measurement technique, Journal of Aerosol Science, Volume 178,2024,106336,ISSN 0021-8502, https://doi.org/10.1016/j.jaerosci.2024.106336.

## WMS DATA"README_WMS.txt": Description of data matrix "WMS.csv" and data format "WMS.zip"

## AEROSOL DATA"README_Aerosol.txt": Description of data matrix "Aerosol.csv" and data format "Aerosol.zip"
DOI: 10.5281/zenodo.17662345
title: Database experimental data "Two-phase hydrodynamics and aerosol mass transfer characterization in pool scrubbing: a simultaneous measurement technique"

description: ## DATABASE EXPERIMENTAL DATA "TWO-PHASE HYDRODYNAMICS AND AEROSOL MASS TRANSFER CHARACTERIZATION IN POOL SCRUBBING: A SIMULTANEOUS MEASUREMENT TECHNIQUE"Reference Open-Access journal publication: Alvaro Ramos Perez, Terttaliisa Lind, Victor Petrov, Annalisa Manera, Horst-Michael Prasser,Two-phase hydrodynamics and aerosol mass transfer characterization in pool scrubbing: A simultaneous measurement technique, Journal of Aerosol Science, Volume 178,2024,106336,ISSN 0021-8502, https://doi.org/10.1016/j.jaerosci.2024.106336.

## WMS DATA"README_WMS.txt": Description of data matrix "WMS.csv" and data format "WMS.zip"

## AEROSOL DATA"README_Aerosol.txt": Description of data matrix "Aerosol.csv" and data format "Aerosol.zip"
DOI: 10.5061/dryad.8sf7m0cqp
title: Data from: Classifying interactions in a synthetic bacterial community is hindered by inhibitory growth medium

description: Predicting the fate of a microbial community and its member species relies
 on understanding the nature of their interactions. However, designing
 simple assays that distinguish between interaction types can be
 challenging. Here, we performed spent media assays based on the
 predictions of a mathematical model to decipher the interactions between
 four bacterial species: Agrobacterium tumefaciens (At), Comamonas
 testosteroni (Ct), Microbacterium saperdae (Ms) and Ochrobactrum anthropi
 (Oa). While most experimental results matched model predictions, the
 behavior of Ct did not: its lag phase was reduced in the pure spent media
 of At and Ms, but prolonged again when we replenished with our growth
 medium. Further experiments showed that the growth medium actually delayed
 the growth of Ct, leading us to suspect that At and Ms could alleviate
 this inhibitory effect. There was, however, no evidence supporting such
 "cross-detoxification" and instead, we identified metabolites
 secreted by At and Ms that were then consumed or "cross-fed" by
 Ct, shortening its lag phase. Our results highlight that even simple,
 defined growth media can have inhibitory effects on some species and that
 such negative effects need to be included in our models. Based on this, we
 present new guidelines to correctly distinguish between different
 interaction types, such as cross-detoxification and cross-feeding.
description: All the data that were used to generate the figures (and supp.
 figures) of the paper. This includes: - OD600 / CFUs
 data - Metabolomics data - Chemical
 quantifications from commercial kits
description: For the chemical kits, please refer to their protocol from the
 vendor (exact product numbers are available in the manuscript).
DOI: 10.5061/dryad.wh70rxwq3
title: Leap-frog migration and residents: new migratory habits in Swedish Greylag geese

description: Knowledge about intraspecific and individual variation in bird migration
 behavior is important to predict spatiotemporal distribution, patterns of
 phenology, breeding success and interactions with the surrounding
 environment (e.g., human livelihoods). Such variation is key to adaptive,
 evolutionary responses, i.e., how individuals respond spatiotemporally to
 the environment to maximize fitness. In this study we used GPS location
 data from one to three full annual cycles from 76 Greylag geese Anser
 anser to test the hypothesis that geese originating at five latitudinally
 separated capture sites in Sweden have different migration strategies. We
 also assessed individual consistency in movement strategy over consecutive
 annual cycles. We used the scale-independent net squared displacement
 modelling framework to quantify variables of autumn and spring migration
 for geese from each capture site: distance, timing, and duration. Our
 results demonstrate a positive correlation between migration distance and
 latitudinal origin. Geese from the northernmost site on average migrated
 farther south and about 15 times as far as the short-moving or resident
 geese from the two southernmost sites. Movement strategies of individual
 geese varied considerably both within and among capture sites. Individual
 consistency in movement strategy from one annual cycle to the consecutive
 was high in geese from the northern sites moving the farthest, whereas the
 resident or short-moving geese from the southernmost sites generally
 showed lower or no individual consistency. These changes have come about
 during a time span so short (i.e. ca 35 years or 8-10 generations) that it
 can unlikely be explained by classical Darwinian between-generation
 adaptation. Consequently, and given that young geese follow their parents
 during their first migration, we presume an important role of
 within-family, inter-generation change as a driver behind the large-scale
 changed migration habits in Swedish Greylag geese.
description: The study is based on location
 data obtained 2017-2020 from 76 Greylag geese with GPS-equipped neckbands,
 made by either Ornitela (OT-N35 and OT-N44) or Made-by-Theo (Theo
 Gerrits), focusing on breeding and molting adults and their unfledged
 goslings. Handling protocols were approved by the animal ethics committee
 for central Sweden and fulfilled the ethical requirements for research on
 wild animals (decision Dnr 5.8.18-03584/2017). The GPS location dataset
 was handled and analysed according to the framework of net squared
 displacement modelling. For detailed methods, see the focal paper
 or <em>Bunnefeld et al. 2011. A model-driven approach to quantify migration
 patterns: individual, regional and yearly differences. - J. Anim. Ecol.
 80: 466–476.</em>
DOI: 10.5061/dryad.ht76hdrhx
title: Source data for: Nesting success of Red-winged Blackbirds (Agelaius phoeniceus) in marshes in an anthropogenic landscape

description: Recent analyses show significant population declines in many abundant
 avian species, especially marsh-nesting species including the Red-winged
 Blackbird (RWBL). Hypothesized causes include reduced nesting success
 resulting from changing land use patterns and exposure to contaminants.
 Our goal was to test the hypothesis that landscape and nest
 characteristics as well as exposure to polychlorinated biphenyls (PCBs)
 correlate with nesting success. From 2008-2014, we measured clutch size,
 egg and nestling mass, hatching and fledging success, and daily survival
 of 1293 RWBL nests from 32 marshes in the Hudson River valley of New York.
 Using generalized linear effect and survival models, we found that: (1)
 Julian date was negatively related to hatching success and clutch size but
 positively related to egg mass; (2) nest height was negatively related to
 hatching success; (3) nestling mass decreased with increased nest density
 and distance to edges; (4) fledging success was significantly lower in
 nests closer to the ground that were far from water; and (5) clutch size
 and daily survival were higher in nests farther from  water.
 Results showed that nesting success was correlated with variables
 associated with flooding, population density, and predation and provided
 no support for the predicted negative effects of PCB exposure.
DOI: 10.15468/dl.d4vw6u
title: Occurrence Download

description: A dataset containing 285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gelidium divaricatum"
 ]
}

 The dataset includes 285 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003071-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s4mw6m981
title: Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus)

description: Cycles of glacial expansion and contraction throughout the Pleistocene
 drove increases and decreases, respectively, in the geographical range and
 population size of many animal species. Genetic data have revealed that
 during glacial maxima the distribution of many Eurasian animals was
 restricted to small refugial areas, from which species expanded to
 reoccupy parts of their former range as the climate warmed. It has been
 suggested that the extinct eastern moa (Emeus crassus)—a large, flightless
 bird from New Zealand—behaved analogously during glacial maxima, possibly
 surviving only in a restricted area of lowland habitat in the southern
 South Island of New Zealand during the Last Glacial Maximum (LGM).
 However, previous studies have lacked the power and geographic sampling to
 explicitly test this hypothesis using genetic data. Here we analyse 46
 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of
 the eastern moa from across their post-LGM distribution. Our results are
 consistent with a post-LGM increase in the population size and genetic
 diversity of eastern moa. We also demonstrate that genetic diversity was
 higher in eastern moa from the southern extent of their range, supporting
 the hypothesis that they expanded from a single glacial refugium following
 the LGM.
DOI: 10.5061/dryad.3j9kd51m2
title: Multiple-batch spawning: a risk spreading strategy disarmed by highly intensive size-selective fishing

description: Here we upload the files that support our research on the role of
 risk-spreading strategies in the light of fisheries-induced evolution. The
 code is stored in Zenodo. Abstract from the paper: Can the advantage of
 risk-managing life-history strategies become a disadvantage under
 human-induced evolution? Organisms have adapted to the variability and the
 uncertainty of environmental conditions with a vast diversity of
 life-history strategies. One of such evolved strategies is multiple-batch
 spawning, a spawning strategy common to long-lived fishes that ‘hedge
 their bets’, by distributing the risk to their offspring on a temporal and
 spatial scale. The fitness benefits of this spawning strategy increase
 with female body size, the very trait that size-selective fishing targets.
 By applying an empirically and theoretically motivated eco-evolutionary
 mechanistic model that was parameterized for Atlantic cod (Gadus morhua),
 we explored how fishing intensity may alter the life-history traits and
 fitness of fishes that are multiple-batch spawners. Our main findings are
 twofold; first, the risk-spreading strategy of multiple-batch spawning is
 not effective against fisheries selection, because the fisheries selection
 favours smaller fish with lower risk-spreading effect,
 and second, the ecological recovery in population size does not
 secure evolutionary recovery in the population size structure. The
 beneficial risk-spreading mechanism of the batch spawning strategy
 highlights the importance of recovery in the size structure of overfished
 stocks, from which a full recovery in the population size can follow.
description: We used the empirically-motivated individual-based
 eco-evolutionary model to simulate the dataset.
description: Simulations and data analyses were conducted in the
 open-source statistical programming language R (R Core Team,
 2021).
DOI: 10.5061/dryad.hqbzkh1j3
title: DNA metabarcoding sequence data for diet analysis of caribou

description: Woodland caribou (Rangifer tarandus caribou) are threatened in Canada due
 to the drastic decline in population size caused primarily by
 human-induced landscape changes that decrease habitat and increase
 predation risk. Conservation efforts have largely focused on reducing
 predators and protecting critical habitat, whereas research on dietary
 niches and the role of potential food constraints in lichen-poor
 environments is limited. To improve our understanding of dietary niche
 variability, we used a next-generation sequencing approach with
 metabarcoding of DNA extracted from faecal pellets of woodland caribou
 located on Lake Superior in lichen-rich (mainland) and lichen-poor
 (island) environments. Amplicon sequencing of fungal ITS2 region revealed
 lichen-associated fungi as predominant in samples from both populations,
 but amplification at the chloroplast trnL region, which
 was only successful on island samples, revealed primary consumption of yew
 based on relative read abundance (Taxus spp.; 83.68%) with dogwood (Cornus
 spp.; 9.67%) and maple (Acer spp.; 4.10%) also prevalent. These results
 suggest that conservation efforts for caribou need to consider the
 availability of food resources beyond lichen to ensure successful
 outcomes.  More broadly, we provide a reliable methodology for
 assessing ungulate diet from archived faecal pellets that could reveal
 important dietary shifts over time in response to climate change.
description: Methodological details are contained in the original publication.
 All data were generated on an Illumina MiSeq platform.
DOI: 10.25349/d93w5b
title: The order Axinellida in California

description: Sponges are common and diverse in California, but they have received
 little study in the region, and the identities of many common species
 remain unclear. Here we combine fresh collections and museum vouchers to
 revise the order axinellida for California. Seven new species are
 described: Endectyon (Endectyon) hispitumulus, Eurypon curvoclavus,
 Aulospongus viridans, Aulospongus lajollaensis, Halicnemia
 litorea, Halicnemia montereyensis, and Halicnemia
 weltoni. One new combination is also described, and two existing species
 are reduced to junior synonyms, resulting in a total of 13 species; a
 dichotomous key to differentiate them is provided. DNA data from 9 of the
 13 species are combined with publicly available data to produce updated
 global phylogenies for the order.
description: Spicule measurements were made on images using ImageJ, after
 calculating the number of pixels per mm with a calibration slide. Unless
 otherwise specified, spicule length was measured as the longest possible
 straight line from tip to tip, even when spicules were curved or bent.
 Spicule width was measured at the widest point, excluding adornments like
 swollen tyles. Other files are metadata and supplementary figures from the
 associated manuscript.
description: README file included as Readme.txt
DOI: 10.5061/dryad.cz8w9gj5d
title: Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

description: Molecular dating methods of population splits are crucial in evolutionary
 biology, but they present important difficulties due to the complexity of
 the genealogical relationships of genes and past migrations between
 populations. Using the double digest restriction-site associated DNA
 (ddRAD) technique and an isolation-with-migration (IM) model, we studied
 the evolutionary history of water vole populations of the
 genus Arvicola, a group of complex evolution with fossorial and
 semi-aquatic ecotypes. To do this, we first estimated mutation rates of
 ddRAD loci using a phylogenetic approach. An IM model was then used to
 estimate split times and other relevant demographic parameters. A set of
 300 ddRAD loci that included 85 calibrated loci resulted in good mixing
 and model convergence. The results showed that the two populations
 of A. scherman present in the Iberian Peninsula split 34
 thousand years ago, during the last glaciation. In addition, the much
 greater divergence from its sister species, A. amphibius, may
 help to clarify the controversial taxonomy of the genus. We conclude that
 this approach, based on ddRAD data and an IM model, is highly useful for
 analyzing the origin of populations and species.
description: <strong>Quality-filtered reads for each sample in FASTQ
 format.</strong> ddRAD_reads.zip
 <strong>Rodent alignments used for calibration in NEXUS
 format.</strong> BEAST_alignments.zip
DOI: 10.5281/zenodo.18399851
title: Dataset for paper "Charge-induced ultralow friction between graphite and atomically flat surfaces" (https://doi.org/10.1016/j.carbon.2024.119036)
DOI: 10.5281/zenodo.18399852
title: Dataset for paper "Charge-induced ultralow friction between graphite and atomically flat surfaces" (https://doi.org/10.1016/j.carbon.2024.119036)
DOI: 10.5061/dryad.612jm6457
title: A dynamic ancestral graph model and GPU-based simulation of a community based on metagenomic sampling

description: In this paper we present an ancestral graph model of the evolution of a
 guild in an ecological community. The model is based on a metagenomic
 sampling design in that a random sample is taken at the community, as
 opposed the taxon, level and species are discovered by genetic sequencing.
 The specific implementation of the model envisions an ecological guild
 that was founded by colonization at some point in the past that then
 potentially undergoes diversification by natural selection. Within the
 graph, species emerge and evolve through the diversification process and
 their densities in the graph are dynamic and governed by both ecological
 drift and random genetic drift, as well as differential viability. We
 employ the 3% sequence divergence rule at a marker locus to identify
 Operational Taxonomic Units. We then explore approaches to see if there
 are indirect signals of the diversification process, including population
 genetic and ecological approaches. In terms of population genetics, we
 study the joint site frequency spectrum of OTUs, as well its associated
 statistics. In terms of ecology, we study the species (or OTU) abundance
 distribution. For both we observe deviations from neutrality, which
 indicates that there may be signals of diversifying selection in
 metagenomic studies under certain conditions. The model is available as a
 GPU-based computer program in C/C++ and using OpenCL, with the long-term
 goal of adding functionality iteratively to model large-scale
 eco-evolutionary processes for metagenomic data.
description: The zipped folder in Data Dryad consists of raw simulation
 results and analysis files. A README.txt file provides
 a more detailed explanation of the contents of subfolders. 
 Computer code is provided through Zenodo. An
 associated README.txt file is provided with information on compiling and
 using the program.