cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2jm63xsvd
title: Aquaculture-driven evolution of the salmon louse mtDNA genome

description: Resistance towards the antiparasitic pyrethroid, deltamethrin, is reported
 in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a
 persistent ectoparasite of farmed and wild salmonids. The resistance
 mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers
 for resistance have been identified. Here, we investigated how widespread
 pyrethroid use in aquaculture may have influenced mtDNA variation in lice,
 and the dispersion of resistant haplotypes across the North Atlantic,
 using historical (2000–2002 “pre-resistance”) and contemporary (2014–2017
 “post-resistance”) samples. To study this, we sequenced ATPase 6 and
 cytochrome b, genotyped two genetic markers for deltamethrin resistance,
 and genotyped microsatellites as “neutral” controls of potential
 population bottlenecks. Overall, we observed a modest reduction in mtDNA
 diversity in the period 2000–2017, but no reduction in microsatellite
 variation was observed. The reduction in mtDNA variation was especially
 distinct in two of the contemporary samples, fixed for one and two
 haplotypes respectively. By contrast, all historical samples consisted of
 close to one mtDNA haplotype per individual. No population genetic
 structure was detected among the historical samples for mtDNA nor
 microsatellites. By contrast, significant population genetic
 differentiation was observed for mtDNA among some of the contemporary
 samples. However, the observed population genetic structure was tightly
 linked with the pattern of deltamethrin resistance, and we therefore
 conclude that it primarily reflects the transient mosaic of pyrethroid
 usage in time and space. Two historically undetected mtDNA haplotypes
 dominated in the contemporary samples, both of which were linked to
 deltamethrin resistance, demonstrating primarily two origins of
 deltamethrin resistance in the North Atlantic. Collectively, these data
 demonstrate that the widespread use of pyrethroids in commercial
 aquaculture has substantially altered the patterns of mtDNA diversity in
 lice across the North Atlantic, and, that long-distance dispersion of
 resistance is rapid due to the high level of genetic connectivity that is
 observed in this species.
description: The genotyped resistance data
 for deltamethrin and organophosphate of salmon lice collected in the
 Northern Atlantic during the time frame of 2014 to 2017, combined with the
 mitochondrial sequences using Sanger sequencing technique for both the
 mitochondrial genes ATPase 6 and Cytochrome b are available in the Excel
 file Resistance_mitochondrial_data.xls.
 In addition, microsatellite genotypes of salmon lice collected in the time
 frame 2000 to 2017 in the Northern Atlantic, are available in the Excel
 file Microsatellite_data.xls.
DOI: 10.5061/dryad.gf1vhhmv7
title: NGS data from: Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

description: Fine-tuning of protein-protein interactions occurs naturally through
 coevolution, but this process is difficult to recapitulate in the
 laboratory. We describe a synthetic platform for protein-protein
 coevolution that can isolate matched pairs of interacting muteins from
 complex libraries. This large dataset of coevolved complexes 
 drove a systems-level analysis of molecular recognition between Z
 domain-affibody pairs spanning a wide range of structures, affinities,
 cross-reactivities, and orthogonalities, and captured a broad spectrum of
 coevolutionary networks. Furthermore, we harnessed pre-trained protein
 language models to expand, in silico, the amino acid diversity of our
 coevolution screen, predicting remodeled interfaces beyond the reach of
 the experimental library. The integration of these approaches provides a
 means of generating protein complexes with diverse molecular recognition
 properties as tools for biotechnology and synthetic biology.
description: The Z domain-affibody coevolution library data from the paper was
 obtained using an Illumina MiSeq sequencer. The sequencing data was
 processed to extract the sequences corresponding to the library positions
 in each Z-A and Z-B pair. The raw next-generation sequencing (NGS) data
 was parsed to retrieve the relevant information. Specifically, the
 sequences from Z-A were captured in the first column, followed by the
 sequences from Z-B in the second column, and the corresponding read counts
 were recorded in the third column from the uploaded csv files. This
 parsing process allowed for the extraction of the specific sequences
 present in the coevolution library and the quantification of their
 abundance through read counts. By analyzing this dataset, the study was
 able to investigate the coevolution patterns between Z-A and Z-B and
 examine the interplay of mutations on protein-protein
 interactions.
description: All further data processing, filtering, and analysis steps were
 performed as described in the paper. Data and codes for MI, coevolution
 analysis, and deep learning model are available at
 https://github.com/akds/CoevolveML.
DOI: 10.6071/m36q39
title: Data from: where the minor things are: a pan-eukaryotic survey suggests neutral processes may dominate minor spliceosomal intron evolution

description: Spliceosomal introns are gene segments removed ("spliced") from
 RNA transcripts by large ribonucleoprotein machineries called
 spliceosomes. In some eukaryotes a second spliceosome (the minor/
 U12-type) is responsible for processing a tiny minority of introns.
 Despite its seemingly modest role, minor splicing has persisted for
 roughly 1.5 billion years of eukaryotic evolution. Identifying and
 cataloging minor introns in &gt; 3000 eukaryotic genomes, we report
 diverse evolutionary histories including surprisingly high numbers of
 minor introns in some fungi and green algae, repeated massive loss, as
 well as several general biases in the positional and genic distributions
 of minor introns. We estimate that ancestral minor intron densities were
 comparable to those of the most minor intron-rich species, suggesting a
 trend of long-term stasis. Finally, three findings suggest a major role
 for neutral processes in minor intron evolution. First, we find highly
 similar patterns of minor and major intron evolution, in contrast to the
 predictions of both functionalist and deleterious models. Second, we find
 that observed functional biases among minor intron-containing genes are
 largely explained by these genes' greater ages. Third, we find no
 association of intron splicing with cell proliferation in a minor
 intron-rich fungus, suggesting that regulatory roles are lineage-specific
 and thus cannot offer a general explanation for minor splicing's
 persistence. These data constitute the most comprehensive view to date of
 modern minor introns, their evolutionary history, and the forces shaping
 minor splicing, and provide a foundation for future studies of these
 remarkable genomic elements.
description: This data is a combination of publicly-available annotated genome
 data from resources such as NCBI, Ensembl and JGI, as well as novel
 information related to the classification of intron sequences as either
 major (U2)- or minor (U12)-type. The classification data was obtained
 using intronIC (https://github.com/glarue/intronIC). The archive data is formatted as a single SQLite database file, and includes metadata about introns, transcripts (mRNAs) and genomes from minor-intron-containing species.
description: The database was formatted as a single SQLite database using the
 open-source tool Datasette (https://datasette.io/,
 https://github.com/simonw/datasette). Any tool that can read SQLite data should be able to interface with the database. The simplest method, however, is to use Datasette itself to explore the data locally (an online version of the same data is available at https://www.introns.info), which requires the installation of Datasette (see README file for overview).
DOI: 10.5061/dryad.bvq83bkfs
title: Breeding biology and nesting behaviour of the endemic subspecies of White-eyed Vireo (Vireo griseus bermudianus) on the Bermuda archipelago

description: See full abstract by searching the title of this article on the Journal of
 Field Ornithology webpage, ResearchGate, or Google Scholar. 
description: This research paper was completely descriptive, therefore, there
 is no R-code associated with it; all descriptive stats were done in Excel
 using built-in formulas. This spreadsheet contains descriptive data
 transcribed from field diaries belonging to the primary author, as part of
 his doctoral thesis. The data was collected over a 6-year period of
 watching and recording the breeding behaviour of an endemic subspecies of
 White-eyed Vireo that lives on the Bermuda archipelago. More details on
 how nest observations were recorded in the field can be found in the
 "METHODS" section of the manuscript.  A brief
 summary of the Excel spreadsheet tabs is as follows:  
 "Breeding Data" has rows that summarizes important
 information pertaining to each vireo nest,
 "Breeding Duration" has estimates of when certain
 phases of the nesting cycle started and finished for each nest,
 "Breeding Duration Stats" provides summary statistics
 calculated from the previous tab, "Time Since
 Last Nest" has calculations on the duration between successive nest
 attempts among nesting pairs, "Nest Traits"
 summarizes tree species and physical measurements of each vireo
 nest, "Phenology Data" shows the number of
 occurences of specific nesting stages across breeding seasons; this is
 also the raw data for Figure 3, "Nest Summary
 Stats" has descriptive statistics calculated from tab 5, 
 "Egg Measurements" has the measurement data of several
 vireo eggs,  "Pair Duration" shows the
 estimated time banded vireo pairs remained together,
  "Building" shows the calculations about the number of
 times vireos visited their nest during the nest-building phase,
 "Egg Stage" shows the calculations about the duration
 of times vireos incubated eggs. Blue rows denote the end of an incubation
 watch for the monitored nest, and green rows correspond to when a
 changeover occurred during that incubation watch,
 "Chick Stage" shows the calculations about the number
 of times visiting vireos returned to the nest to feed their young. Blue
 row denotes the end of the observation period for the nest. 
description: The only program needed to open the dataset is Microsoft
 Excel.
DOI: 10.5061/dryad.jh9w0vtgw
title: New key management scheme lattice-based for wireless sensor networks

description: The cluster structure can effectively reduce the cost of mutual
 authentication of sensor nodes, which is conducive to the expansion of the
 network, and can guarantee the security of authentication between sensor
 nodes even in the post-quantum era. The size of the lattice-based
 authentication proposed in this paper does not change much with the
 continuous improvement of the security level of the RSA algorithm. The
 size of the certificate is kept at a stable level, which is more suitable
 for encrypting large data at a high-security level.
description: The authentication sizes
 corresponding to different security levels (such as 64bits, 128bits,
 192bits, 256bits, 320bits, 384bits,448bits, and 512bits) can be calculated
 when the selected system parameter is
 n=256bits, q=2**32.
DOI: 10.5061/dryad.jh9w0vtgx
title: Effects of biochar amendment on daily CO2 emission

description: Poplar residue-derived biochars were larger in surface area and total pore
 volume but lower in nutrients and pH values than the rice straw-derived
 biochar. Increasing pyrolysis temperature led to a decrease in the total
 nitrogen content (TN) of poplar leaf- and rice straw-derived biochars, but
 enhanced the TN in the poplar twig- and poplar bark-derived biochars.
 After 180-day incubation, the total cumulative CO2 emission
 decreased by 33.1–73.8% in the biochar amendments compared to their
 corresponding biomass residue addition, whereas the biochars derived from
 poplar twig and bark residues had more positive effects on reducing soil
 CO2 emissions, but depended on the pyrolysis temperature.
description: Here, a laboratory incubation study was conducted to assess the
 effects of different biochars and their corresponding biomass residues on
 soil CO<sub>2</sub> emissions during the 180 days of
 incubation.  Three types of poplar residues were
 sampled from a Nanlin-895
 (<em>Populus </em>× <em>euramericana</em> cv.
 ‘Nanlin-895’) plantation established in March 2007, named as twig residue
 (the largest diameter of twigs &lt; 3 cm, TR), bark residue (BR) and
 leaf residue (LR), respectively. Meanwhile, the residue of rice straw (SR)
 was collected from the farmland near the poplar plantation.
 Biochars were prepared from the residue powders of poplar twig,
 bark, and leaf and rice straw using slow pyrolysis method (heating rate
 10 ℃·min<sup>-1</sup>) at 300, 500 and 700 ℃ and residence
 time of 4 h in a condition of hypoxia. These biochars are named in this
 study as follows: T1 (biochar pyrolyzed at 300℃), T2 (biochar pyrolyzed at
 500℃) and T3 (biochar pyrolyzed at 700℃) for poplar twig residue,
 respectively. Similarly, the biochars prepared for other residues are
 named as B1, B2, and B3 for poplar bark residue, L1, L2, and L3 for poplar
 leaf residue, as well as S1, S2, and S3 for rice straw residue,
 respectively.
DOI: 10.15468/dl.yqq6q3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Arion vulgaris, Arion vulgaris x Arion rufus, Arion vulgaris x Arion ater, Arion rufus vulgaris, Arion rufus vulgaris, Arion)",
 "Year 2010-2015"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003546-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dz08kps2s
title: Cortical topographic motifs emerge in a self-organized map of object space

description: The human ventral visual stream has a highly systematic organization of
 object information, but the causal pressures driving these topographic
 motifs are highly debated. Here, we use self-organizing principles to
 learn a topographic representation of the data manifold of a deep neural
 network representational space. We find that a smooth mapping of this
 representational space showed many brain-like motifs, with large-scale
 organization by animacy and real-world object size, supported by mid-level
 feature tuning, with naturally emerging face- and scene-selective regions.
 While some theories of the object-selective cortex posit that these
 differently tuned regions of the brain reflect a collection of distinctly
 specified functional modules, the present work provides computational
 support for an alternate hypothesis that the tuning and topography of the
 object-selective cortex reflects a smooth mapping of a unified
 representational space.
DOI: 10.15468/dl.d7vaps
title: Occurrence Download

description: A dataset containing 834 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.13.12_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Oxyura leucocephala, Aythya baeri, Mergus squamatus, Anser fabalis, Mareca falcata, Cygnus columbianus, Leucogeranus leucogeranus, Platalea minor, Ciconia nigra, Chroicocephalus ridibundus, Recurvirostra avosetta, Vanellus vanellus)",
 "Year 2020-2025"
 ]
}

 The dataset includes 834 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003550-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k0p2ngfdc
title: Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management

description: Extensive applications of fishery stock enhancement worldwide bring up
 broad concerns about its negative effects, creating a pivotal need for
 science-based assessment and planning of enhancement strategies. However,
 the lack of mechanistic understanding of enhanced population dynamics,
 particularly the density-dependent processes, leads to compromise in model
 development and limits the capacity in predicting enhancement effects.
 Here, we developed an individual-based model based on dynamic energy
 budget theory and full life history processes, to understand the mechanism
 of density dependence in population dynamics that emerge from
 individual-level processes. We demonstrated the utility of the model
 framework by applying it to an extensively enhanced species, Chinese prawn
 (Fenneropenaeus chinensis, Penaeidae). The model could yield projections
 reflecting the observed trajectory of population biomass and yields. The
 model also delineated the key effects of density dependence on the vital
 rates of growth, fecundity, and starvation mortality. Regarding the
 manifold effects of stock enhancement, we demonstrated a dampened shape in
 population biomass and yields with increasing magnitude of enhancement,
 and trade-offs between the ecological and economic objectives,
 i.e., pursuing high benefit might compromise the wild population without
 proper management. Furthermore, we illustrated the possibility of
 combining stock enhancement and harvest regulation in promoting population
 recovery while maintaining fisheries yields. We highlight the potential of
 the proposed model for understanding density dependence in enhancement
 program, and for designing integrated management strategies. The approach
 developed herein may serve as a general approach to assess the population
 dynamics in stock enhancement and inform enhancement management.
DOI: 10.5061/dryad.jh9w0vtgz
title: Fitness and niche differences are both important in explaining responses of plant diversity to nutrient addition

description: Plant species loss due to eutrophication is a common phenomenon in
 temperate perennial grasslands. It occurs in a non-random fashion and is
 usually explained by increased competitive size asymmetry between
 co-occurring winner (tall species with optima in productive habitats) and
 loser species (small-statured plants typical for unproductive habitats).
 It remains unclear why nutrient addition decreases diversity in
 communities consisting of losers only, whereas it has little effect on
 winner-only communities. Here, I used the framework of modern coexistence
 theory to explore fertilization-driven changes in fitness and niche
 differences between different combinations of field-identified winner (W)
 and loser (L) species. I experimentally estimated competition parameters
 for plant species pairs constructed from a pool of eight species,
 including pairs of species from the same (WW, LL) and different species
 categories (LW) grown for approximately two years in control and
 fertilized conditions. Concurrently, I also followed plant species
 diversity in mesocosm communities constructed from the same species pool
 (four-species communities including winners, losers, or both) exposed to
 control and nutrient addition. I found that nutrient addition can reduce
 but, unexpectedly, also promote species coexistence depending on the type
 of species pairs. Whereas nutrient addition eroded coexistence of losers
 with winners, but also with other losers, treatment had the opposite
 effect on the persistence of winner species. Fertilization induced large
 fitness differences between species in loser-winner and loser-loser
 combinations, but had little effect on the fitness differences of species
 within the winner-winner combination. In addition, the persistence of
 winner pairs was promoted by larger niche differences compared to loser
 species, irrespective of soil nutrients. The differences in how nutrient
 addition modified coexistence at the pairwise level were reflected by
 differences in evenness of multispecies communities assembled from the
 corresponding species categories. These results suggest that the effect of
 eutrophication on plant species richness cannot simply be explained by an
 increased competitive asymmetry. To fully understand the effect of
 fertilization on the diversity of temperate grasslands, interspecific and
 intraspecific interactions should be explored while considering
 differences in species’ ecological optima.
DOI: 10.5061/dryad.pk0p2ngtg
title: Data from: Additive genetic and environmental variation interact to shape the dynamics of seasonal migration in a wild bird population

description: Dissecting joint micro-evolutionary and plastic responses to environmental
 perturbations requires quantifying interacting components of genetic and
 environmental variation underlying expression of key traits. This ambition
 is particularly challenging for phenotypically discrete traits where
 multiscale decompositions are required to reveal non-linear
 transformations of underlying genetic and environmental variation into
 phenotypic variation, and when effects must be estimated from incomplete
 field observations. We devised a joint multistate capture-recapture and
 quantitative genetic animal model and fitted this model to
 full-annual-cycle resighting data from partially-migratory European shags
 (Gulosus aristotelis) to estimate key components of genetic, environmental
 and phenotypic variance in the ecologically critical discrete trait of
 seasonal migration versus residence. We demonstrate non-negligible
 additive genetic variance in latent liability for migration, resulting in
 detectable micro-evolutionary responses following two episodes of strong
 survival selection. Further, liability-scale additive genetic effects
 interacted with substantial permanent individual and temporary
 environmental effects to generate complex non-additive effects on
 expressed phenotypes, causing substantial intrinsic gene-by-environment
 interaction variance on the phenotypic scale. Our analyses therefore
 reveal how temporal dynamics of partial seasonal migration arise from
 combinations of instantaneous micro-evolution and within-individual
 phenotypic consistency, and highlight how intrinsic phenotypic plasticity
 could expose genetic variation underlying discrete traits to complex forms
 of selection.
description: The present
 repository contains the dataset in ".csv" format (see details in
 'README' file). A second repository contains the code for
 reading in this file and running the analyses (hosted by Zenodo). A third
 repository contains supplementary files produced by the code for the main
 analyses, which include the complete model outputs and detailed numerical
 summaries (hosted by Zenodo).