cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j2n732c
title: Data from: Pet problems: biological and economic factors that influence the release of alien reptiles and amphibians by pet owners

description: 1. The number of alien reptiles and amphibians introduced and established
 worldwide has been increasing over the last decades. The legal pet trade
 is the now the dominant pathway by which individuals of these species
 arrive in their non-native locale. Despite its importance, pet trade
 pathway specific factors that influence the release (introduction) of
 exotic reptiles and amphibians have not yet been examined. 2. To address
 this gap, we set out to identify broad-scale and easily measured
 biological and economic factors that influence the release of these exotic
 pets by their owners. We hypothesize that biological factors reflect the
 cost of care and economic factors reflect the value owners place on their
 pet, both of which can influence the probability a pet is released. We
 collected life history and economic data on the 1722 species of reptiles
 and amphibians sold within the US as pets over the last 18 years. We also
 compiled a list of pet-trade attributed releases in the US (i.e. all
 free-living species regardless of whether they successfully established).
 We then used boosted regression trees to correlate species release status
 to their life history traits and economic attributes (r2 = 0.51, AUC =
 0.89). 3. We found that species with a high probability of being released
 were imported at higher quantities over our period of record, have a
 relatively large adult mass, and commanded cheaper retail prices. Quantity
 imported and price interact with longevity and adult mass to produce
 non-linear increases in release probability. The most important
 interaction revealed that large-bodied species imported in high quantities
 have a three times higher release probability compared to large-bodied
 species imported in lower quantities. 4. Policy implications. Our results
 provide much needed guidance toward targeting exotic pet reptile and
 amphibian species that are at a high risk of being released. In
 particular, species that are both prevalent in the pet trade and are
 large-bodied or long-lived have the highest probability of being released.
 This will aid in developing education and policy solutions aimed at
 decreasing the rate at which these pets are released, thus curtailing the
 invasion process before these species can establish and impacts can occur
description: R scripts and data for
 boosted regression trees modelR project that includes
 R scripts of boosted regression trees analysis and associated
 data/meta-data used to assess factors relating to the releases of exotic
 pet reptiles and amphibian species in the US.stringham_lockwood_2018.zip
DOI: 10.57745/bj7tdv
title: Tig_tig_oak_82kW.dat

description: :unav
DOI: 10.57745/szkllk
title: Tig_tig_beech_60kW.dat

description: :unav
DOI: 10.5061/dryad.pt2g084
title: Data from: Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizards

description: On microevolutionary timescales, adaptive evolution depends upon both
 natural selection and the underlying genetic architecture of traits under
 selection, which may constrain evolutionary outcomes. Whether such genetic
 constraints shape phenotypic diversity over macroevolutionary timescales
 is more controversial, however. One key prediction is that genetic
 constraints should bias the early stages of species divergence along
 “genetic lines of least resistance” defined by the genetic (co)variance
 matrix, G. This bias is expected to erode over time as species means and G
 matrices diverge, allowing phenotypes to evolve away from the major axis
 of variation. We tested for evidence of this signal in West Indian Anolis
 lizards, an iconic example of adaptive radiation. We found that the major
 axis of morphological evolution was well aligned with a major axis of
 genetic variance shared by all species despite separation times of 20-40
 million years, suggesting that divergence occurred along a conserved
 genetic line of least resistance. Further, this signal persisted even as G
 itself evolved, apparently because the largest evolutionary changes in G
 were themselves aligned with the line of genetic least resistance. Our
 results demonstrate that the signature of genetic constraint may persist
 over much longer timescales than previously appreciated, even in the
 presence of evolving genetic architecture. This pattern may have arisen
 either because pervasive constraints have biased the course of adaptive
 evolution or because the G matrix itself has been shaped by selection to
 conform to the adaptive landscape.
description: G matrix pedigrees and
 dataPedigrees and data for
 calculating G matrices and divergence for seven species of Anolis
 lizards.Null distribution of
 anglesNull distribution of
 angles between pairs of randomly generated eight-element vectors with unit
 length.Adult measurements for
 divergenceAdult measurements from
 15 Anolis species for calculating phenotypic divergence
DOI: 10.57745/6vkjtq
title: Tig_tig_beech_82kW.dat

description: :unav
DOI: 10.57745/dxfpfs
title: Tig_tig_spruce_60kW.dat

description: :unav
DOI: 10.57745/kfrl0p
title: Tig_tig_spruce_93kW.dat

description: :unav
DOI: 10.57745/1qison
title: Tig_tig_poplar_82kW.dat

description: :unav
DOI: 10.5061/dryad.k31vr19
title: Data from: Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)

description: This investigation establishes the first sequence-based phylogenetic
 hypothesis of species relationships in the Coca family (Erythroxylaceae).
 We focused our phylogenomic inference on the largest taxonomic section in
 the genus Erythroxylum (Archerythroxylum O. E. Schulz) using concatenation
 and gene tree reconciliation methods from hybridization-based target
 capture of 427 genes. We show that Neotropical Erythroxylum are
 monophyletic within the Paleotropical lineages, yet Archerythroxylum and
 all of the other taxonomic sections from which we sampled multiple species
 lack monophyly. We mapped phytogeographic states onto the tree and found
 some concordance between these regions and clades. The wild species E.
 gracilipes and E. cataractarum are most closely related to the cultivated
 E. coca and E. novogranatense but relationships within this “coca” clade
 remain equivocal, suggesting a more complicated origin than Plowman’s
 single-domestication hypothesis. Our results point to the difficulty of
 morphology-based intrageneric classification in this clade and highlight
 the importance of integrative taxonomy in future systematic revisions. In
 compliance with data protection regulations, please contact the
 publication office if you would like to have your personal information
 removed from the database.
description: Two Erythroxylaceae
 treesAstral II lineage tree
 and ML Concat tree inferred from 427 genes for 81 Erythroxylaceae
 individuals.trees.tar.gzGene alignments and concatenated matrixAlignments for 427 gene trees, concatenated sequence matrix, and concat partition file.alignments.tar.gzSample data spreadsheetSample names, taxonomic section, species geographic region, Genbank biosample name, collector information, herbarium voucher information.White_Archerythroxylum_SampleInfo.xlsx
DOI: 10.57745/k9ueqa
title: Tig_tig_balsa_82kW.dat

description: :unav
DOI: 10.57745/o7sjul
title: ipe_auto_tig=f((rho)_82kW.dat

description: :unav
DOI: 10.57745/q5egz4
title: larch_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/leqfkn
title: larch_auto_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.5061/dryad.95r0850
title: Data from: Food quality and quantity is more important in explaining foraging of an intermediate-sized mammalian herbivore than predation risk or competition

description: During times of high activity by predators and competitors, herbivores may
 be forced to forage in patches of low-quality food. However, the relative
 importance in determining where and what herbivores forage still remains
 unclear, especially for small and intermediate-sized herbivores. Our
 objective was to test the relative importance of predator and competitor
 activity, and forage quality and quantity on the proportion of time spent
 in a vegetation type and the proportion of time spent foraging by the
 intermediate-sized herbivore European hare (Lepus europaeus). We studied
 red fox (Vulpes vulpes) as a predator species and European rabbit
 (Oryctolagus cuniculus) as a competitor. We investigated the time spent at
 a location and foraging time of hare using GPS with accelerometers. Forage
 quality and quantity was analysed based on hand-plucked samples of a
 selection of the locally most important plant species in the diet of hare.
 Predator and competitor activity was investigated using a network of
 camera traps. Hares spent a higher proportion of time in vegetation types
 that contained a higher percentage of fibres (i.e., NDF). Besides, hares
 spent a higher proportion of time in vegetation types that contained
 relatively low food quantity and quality of forage (i.e., high percentage
 of fibres) during days that foxes (Vulpes vulpes) were more active. Also
 during days that rabbits (Oryctolagus cuniculus) were more active, hares
 spent a higher proportion of time foraging in vegetation types that
 contained a relatively low quality of forage. Although predation risk
 affected space use and foraging behaviour, and competition affected
 foraging behaviour, our study shows that food quality and quantity more
 strongly affected space use and foraging behaviour than predation risk or
 competition. It seems that we need to reconsider the relative importance
 of the landscape of food in a world of fear and competition.
description: Database_Hare_foraging
 behaviour_3_7_2018collected in the field
 by collared aninmals, camera trap data and vegetation
 samplesDatabase_Hare_location_3_7_2018Collected in the field by collared animals, camera trap data and vegetation samplesR script_Hare_foraging behaviour_3_7_2018R script_Hare_location_3_7_2018
DOI: 10.57745/3fddlg
title: 00_README.txt

description: :unav
DOI: 10.5281/zenodo.18389485
title: P Retention in Ditches & Ponds

description: Dataset on phosphorus retention in agricultural ditches and ponds, compiled from CNKI and Web of Science studies
DOI: 10.5281/zenodo.18389486
title: P Retention in Ditches & Ponds

description: Dataset on phosphorus retention in agricultural ditches and ponds, compiled from CNKI and Web of Science studies
DOI: 10.5061/dryad.tf56fm1
title: Data from: Finding flies in the mushroom soup: host specificity of fungus-associated communities revisited with a novel molecular method

description: Fruiting bodies of fungi constitute an important resource for thousands of
 other taxa. The structure of these diverse assemblages has traditionally
 been studied with labour-intensive methods involving cultivation and
 morphology-based species identification, to which molecular information
 might offer convenient complements. To overcome challenges in DNA
 extraction and PCR associated with the complex chemical properties
 fruiting bodies, we developed a pipeline applicable for extracting
 amplifiable total DNA from soft fungal samples of any size. Our protocol
 purifies DNA in two sequential steps: (1) initial salt-isopropanol
 extraction of all nucleic acids in the sample is followed by (2) an extra
 clean-up step using solid-phase reversible immobilization (SPRI) magnetic
 beads. The protocol proved highly efficient, with practically all of our
 samples — regardless of biomass or other properties — being successfully
 PCR amplified using metabarcoding primers and subsequently sequenced. As a
 proof-of-concept, we apply our methods to address a topical ecological
 question: is host specificity a major characteristic of fungus-associated
 communities, i.e., do different fungus species harbour different
 communities of associated organisms? Based on an analysis of 312 fungal
 fruiting bodies representing ten species in five genera from three orders,
 we show that molecular methods are suitable for studying this rich natural
 microcosm. Comparing to previous knowledge based on rearing and
 morphology-based identifications, we find a species-rich assemblage
 characterized by a low degree of host specialization. Our method opens up
 new horizons for molecular analyses of fungus-associated interaction webs
 and communities.
description: CO1
 taxonomyThe taxonomy matrix used
 to identify taxa in CO1 analyses of the article.co1_taxonomy.csv16S taxonomyThe 16S (bacterial) taxonomy and OTU names used in the article.16s_taxonomy.csvITS taxonomyThe ITS (fungal) taxonomy and OTU names used in the article.its_taxonomy.csvCommunity raw dataExcel file containing the raw read numbers, as well as dubious sample information.community_rawdata.xlsxAnalytical scriptsA compressed folder including the scripts, as well as final datasets for HMSC models.READMEReadme for contents of this Dryad package.
DOI: 10.5061/dryad.rc78g29
title: Data from: Mutation accumulation in selfing populations under fluctuating selection

description: Selfing species are prone to extinction, possibly because highly selfing
 populations can suffer from a continuous accumulation of deleterious
 mutations, a process analogous to Muller’s ratchet in asexual populations.
 However, current theory provides little insight into which types of genes
 are most likely to accumulate deleterious alleles and what environmental
 circumstances may accelerate genomic degradation. Here we investigate
 temporal changes in the environment that cause fluctuations in the
 strength of purifying selection. We simulate selfing populations with
 genomes containing a mixture of loci experiencing constant selection and
 loci experiencing selection that fluctuates in strength (but not
 direction). Even when both types of loci experience the same average
 strength of selection, loci under fluctuating selection contribute
 disproportionately more to deleterious mutation accumulation. Moreover,
 the presence of loci experiencing fluctuating selection in the genome
 increases the deleterious fixation rate at loci under constant selection;
 under most realistic scenarios this effect of linked selection can be
 attributed to a reduction in N¬e. Fluctuating selection is particularly
 injurious when selective environments are strongly autocorrelated over
 time and when selection is concentrated into rare bouts of strong
 selection. These results imply that loci under fluctuating selection are
 likely important drivers of extinction in selfing species.
description: Ho_and_Agrawal_2018_SimulationDataFile contains data from the simulations.
DOI: 10.5061/dryad.v046c7g
title: Data from: The emergence and selection of reputation systems that drive cooperative behaviour

description: Reputational concerns are believed to play a crucial role in explaining
 cooperative behaviour among non-kin humans. Individuals cooperate to avoid
 a negative social image if being branded as defector reduces pay-offs from
 future interactions. Similarly, individuals sanction defectors to gain a
 reputation as punisher, prompting future co-players to cooperate. But
 reputation can only effectively support cooperation if a sufficient number
 of individuals condition their strategies on their co-players'
 reputation, and if a sufficient number of group members are willing to
 record and transmit the relevant information about past actions. Using
 computer simulations, this paper argues that starting from a pool of
 non-cooperative individuals, a reputation system based on punishment is
 likely to emerge and to be the driver of the initial evolution of
 cooperative behaviour. However, once cooperation is established in a
 group, it will be sustained mainly through a reputation mechanism based on
 cooperative actions.
description: Simulation output
 dataSimulation data using
 benchmark parameters and from all three scenarios as described in the
 paper. Contains data for generations 15001-20000 of 20 simulations for
 each scenario.reputational SI
 simulations.zipSimulation
 codePython code (Python 3)
 used to run all simulations discussed in the paper. The code is fully
 commented and can be executed as is.reput_simulation_code.txt
DOI: 10.5061/dryad.5ph7sm6
title: Data from: Depth image super-resolution reconstruction based on a modified joint trilateral filter

description: Depth image super-resolution (SR) is a technique that utilizes signal
 processing technology to enhance the resolution of a low-resolution (LR)
 depth image. Generally, the external database or high-resolution (HR)
 images are needed for acquiring the priori information to support the SR
 reconstruction. To overcome the limitation, a depth image SR method which
 does not need the reference of any external images is proposed. In the
 paper, a high-quality edge map is firstly constructed using a sparse
 coding method, which uses a dictionary learned from the original images
 themselves at different scales. Then, the high-quality edge map is used to
 guide the interpolation for depth images by a modified joint trilateral
 filter. During the interpolation, some information of gradient and
 structural similarity (SSIM) are added to preserve the detailed
 information and suppress the noise. The proposed method not only can
 preserve the sharpness of image edge, but also can avoid the dependence on
 database. Experimental results show the proposed method is superior to
 some state-of-the-art depth image SR methods.
description: codes and
 datas20181227datas and codes for
 experiment
DOI: 10.5061/dryad.s4n5t51
title: Data from: Remarkably conserved plastid genomes of Quercus Group Cerris in China: comparative and phylogenetic analyses

description: Quercus is one of the most important genera for considering its economic
 and ecological values, with approximately 500 species worldwide. Quercus
 group Cerris is endemic to Eurasia (including 11 species), and three
 species (Quercus acutissima, Quercus chenii and Quercus variabilis) are
 widely distributed in China. Here, we sequenced the complete plastid
 genomes of Q. acutissima and Q. chenii by Illumina pair-end sequencing,
 and obtained an additional plastome of Q. variabilis from GenBank.
 Although geographically distant sampling, the three plastomes in group
 Cerris were remarkably conserved with regard to genome size, gene
 organization, GC content, and IR/SC boundary regions. The phylogenetic
 analysis showed that group Cerris nested in group Ilex, forming a
 Cerris-Ilex clade. The current study provided plastid genomic-scale data
 for the less intensively studied group Cerris, which would be useful for
 studying speciation processes, geographical structure and phylogeny within
 the group Cerris in the future.
description: plastid genome
 sequecesComplete plastid genome
 sequeces of Quercus acutissima and Quercus chenii, the format are .fasta
 and .geneious.Cerris plastid
 data.zip
DOI: 10.5061/dryad.532m1m8
title: Data from: Screening of candidate substrates and coupling ions of transporters by thermostability shift assays

description: Substrates of most transport proteins have not been identified, limiting
 our understanding of their role in physiology and disease. Traditional
 identification methods use transport assays with radioactive compounds,
 but they are technically challenging and many compounds are unavailable in
 radioactive form or are prohibitively expensive, precluding large-scale
 trials. Here, we present a high-throughput screening method that can
 identify candidate substrates from libraries of unlabeled compounds. The
 assay is based on the principle that transport proteins recognize
 substrates through specific interactions, which lead to enhanced
 stabilization of the transporter population in thermostability shift
 assays. Representatives of three different transporter (super)families
 were tested, which differ in structure as well as transport and ion
 coupling mechanisms. In each case, the substrates were identified
 correctly from a large set of chemically related compounds, including
 stereo-isoforms. In some cases, stabilization by substrate binding was
 enhanced further by ions, providing testable hypotheses on energy coupling
 mechanisms.
description: Figure 2
 dataValidation of the method
 for determining substrate specificity using three unrelated
 proteins.Figure
 2.xlsxFigure 3
 dataIdentification of
 substrates for a mitochondrial phosphate carrier from the thermophilic
 ciliate Tetrahymena thermophila.Figure
 3.xlsxFigure 4
 DataThe effect of coupling
 ions on the stabilization of transporters by substrate
 binding.Figure
 4.xlsxFigure 1-figure
 supplement 1Figure 2-figure
 supplement 2Figure 2-figure
 supplement 4Figure 3-figure
 supplement 3
DOI: 10.5061/dryad.8r0m76h
title: Data from: The influence of multiple functional demands on morphological diversification: A test on turtle shells

description: Organismal parts are often involved in the performance of more than one
 function. The role of trade-offs in influencing phenotypic evolution of
 such parts is well-studied; less well-understood is their role in
 influencing phenotypic diversity. Increases in the number of functions a
 part is involved in may inhibit subsequent diversification, as the number
 of trade-offs increases. Alternately, such an increase might promote
 phenotypic diversification, by increasing adaptive landscape complexity
 and promoting specialization for different roles. We compare these
 predictions by testing whether aquatic turtle shells, which resist loads,
 act as hydrodynamic elements, facilitate self-righting, and exchange heat
 with the environment, differ in phenotypic diversity from those of
 terrestrial species, which perform all the same functions except for
 hydrodynamics. We used 53 3D landmarks digitized on 2722 specimens of 274
 hard-shelled turtle species to quantify shell shape variation, and a set
 of phylogenetic hypotheses to examine evolutionary patterns. Terrestrial
 turtles consistently had higher phenotypic diversity than aquatic species.
 Differences are not due to differences in the rates of evolution between
 the two groups, but rather differences in evolutionary mode. Thus this
 study supports the traditional view of the role of multiple functions in
 determining phenotypic diversity.
description: All morphometric
 dataAll landmark coordinate
 data collected to describe variation in turtle shell
 morphology.StaytonO'ConnerNisivoccia2018_SupplementaryFile03.csvPhylogenyConsensus phylogeny used for data visualizationStaytonO'ConnerNisivoccia2018_SupplementaryFile04.nexus