cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1615h
title: Data from: A mathematical understanding of how cytoplasmic dynein walks on microtubules

description: Cytoplasmic dynein 1 is a dimeric motor protein that walks and transports
 intracellular cargos towards the minus end of microtubules. In this
 article we formulate, based on physical principles, a mechanical model to
 describe the stepping behaviour of cytoplasmic dynein walking on
 microtubules from the cell membrane towards the nucleus. Unlike previous
 studies on physical models of this nature, we base our formulation on the
 whole structure of cytoplasmic dynein 1 to include the temporal dynamics
 of the individual subunits such as the cargo (for example an endosome,
 vesicle or bead), two rings of six ATPase domains associated with diverse
 cellular activities (AAA+ rings) and the microtubule binding domains which
 allow dynein to bind to microtubules. This mathematical framework allows
 us to examine experimental observations on dynein across a wide range of
 different species, as well as being able to make predictions on the
 temporal behaviour of the individual components of dynein not currently
 experimentally measured. Furthermore, we extend the model framework to
 include backward stepping, variable step size and dwelling. The power of
 our model is in its predictive nature; first it reflects recent
 experimental observations that dynein walks on microtubules using a weakly
 coordinated stepping pattern with predominantly not passing steps. Second,
 the model predicts that interhead coordination in the ATP cycle of
 cytoplasmic dynein is important in order to obtain the alternating
 stepping patterns and long run lengths seen in experiments.
description: Matlab_codeMatlab codes used to generate all the numerical and statistical analysis carried out in the manuscript.
DOI: 10.5061/dryad.93pj0
title: Data from: "Blood transcriptome sequencing of Common Crossbills (Loxia curvirostra) experimentally infected by the avian malaria parasite Plasmodium relictum (lineage SGS1)" in Genomic Resources Notes accepted 1 June 2013-31 July 2013

description: In order to understand the epidemiology of this avian malaria infections
 both geographically and across host species there is a need of more
 polymorphic markers and knowledge about genes expressed during the
 infection of the host. However, technical difficulties have hindered the
 development of such molecular markers. The main difficulty is the fact
 that the host (birds) has nucleated erythrocytes and there is a 52-fold
 difference in the genome size between the host and the parasite. This has
 caused problems in trying to isolate and amplify novel nuclear genes of
 the avian malaria parasites. In order to overcome this difficulty and gain
 molecular data on nuclear genes we have sequenced blood transcriptomes of
 common crossbills experimentally infected with Plasmodium relictum SGS1
 lineage. During development in the blood, the parasite undergoes several
 cycles of asexual development (erythrocytic merogony) and is invading
 numerous host cells and thus is expected to have a high level of gene
 expression. This data will serve as a resource for researchers interested
 in developing more molecular markers and investigating genes expressed
 during the erythrocytic development of avian malaria parasite. With this
 data we hope to take the first step into the understanding of the
 mechanism behind the exhibited host generalism as well as understanding
 how different avian malaria lineages have spread around the globe.
description: file 1.fas file of assembled
 isotigs. Isotig number correspond to isotig numbers in Table
 1file.fasTable 1Table 2
DOI: 10.5061/dryad.ct5v8
title: Data from: Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude

description: Studies that span entire species ranges can provide insight into the
 relative roles of historical contingency and contemporary factors that
 influence population structure and can reveal patterns of genetic
 variation that might otherwise go undetected. American shad is a wide
 ranging anadromous clupeid fish that exhibits variation in demographic
 histories and reproductive strategies (both semelparity and iteroparity)
 and provides a unique perspective on the evolutionary processes that
 govern the genetic architecture of anadromous fishes. Using 13
 microsatellite loci, we examined the magnitude and spatial distribution of
 genetic variation among 33 populations across the species' range to
 (i) determine whether signals of historical demography persist among
 contemporary populations and (ii) assess the effect of different
 reproductive strategies on population structure. Patterns of genetic
 diversity and differentiation among populations varied widely and reflect
 the differential influences of historical demography, microevolutionary
 processes and anthropogenic factors across the species' range.
 Sequential reductions of diversity with latitude among formerly glaciated
 rivers are consistent with stepwise postglacial colonization and
 successive population founder events. Weak differentiation among U.S.
 iteroparous populations may be a consequence of human-mediated gene flow,
 while weak differentiation among semelparous populations probably reflects
 natural gene flow. Evidence for an effect of reproductive strategy on
 population structure suggests an important role for environmental
 variation and suggests that the factors that are responsible for shaping
 American shad life history patterns may also influence population genetic
 structure.
description: Rangewide American shad
 microsatellite dataMicrosatellite dataset
 for 13 loci genotyped across 33 populations of American shad from across
 the species native range.
DOI: 10.5061/dryad.4t80s
title: Data from: Genetic structure of Pacific trout at the extreme southern end of their native range

description: Salmonid fishes are cold water piscivores with a native distribution
 spanning nearly the entire temperate and subarctic northern hemisphere.
 Trout in the genus Oncorhynchus are the most widespread salmonid fishes
 and are among the most important fish species in the world, due to their
 extensive use in aquaculture and valuable fisheries. Trout that inhabit
 northwestern Mexico are the southernmost native salmonid populations in
 the world, and the least studied in North America. They are unfortunately
 also facing threats to their continued existence. Previous work has
 described one endemic species, the Mexican golden trout (O. chrysogaster),
 and one endemic subspecies, Nelson’s trout (O. mykiss nelsoni), in Mexico,
 but previous work indicated that there is vastly more biodiversity in this
 group than formally described. Here we conducted a comprehensive genetic
 analysis of this important group of fishes using novel genetic markers and
 techniques to elucidate the biodiversity of trout inhabiting northwestern
 Mexico, examine genetic population structure of Mexican trout and their
 relationships to other species of Pacific trout, and measure introgression
 from non-native hatchery rainbow trout. We confirmed substantial genetic
 diversity and extremely strong genetic differentiation present in the
 Mexican trout complex, not only between basins but also between some
 locations within basins, with at least four species-level taxa present. We
 also revealed significant divergence between Mexican trout and other trout
 species and found that introgression from non-native rainbow trout is
 present but limited, and that the genetic integrity of native trout is
 still maintained in most locations. This information will help to guide
 effective conservation strategies for this important group of fishes.
description: Data Archiving-
 GenotypesGenotypes from
 microsatellite and Single Nucleotide Polymorphism loci from all
 populations and speciesDA_genotypes.txtData Archiving- MetadataMetadata associated to the genotypes data fileDA_metadata.xlsx
DOI: 10.5061/dryad.0t67n
title: Data from: Sediment-encased maturation: a novel method for simulating diagenesis in organic fossil preservation

description: Exceptional fossils can preserve diagenetically-altered biomolecules, and
 understanding the pathways to such preservation is vital to utilising
 fossil information in evolutionary and palaeoecological studies.
 Experimental taphonomy explores the stability of tissues during
 microbial/autolytic decay or their molecular stability through maturation
 under high pressure and temperature. Maturation experiments are often
 hampered by the fact that maturation occurs inside sealed containers,
 which does not allow for the loss of labile, mobile, or volatile
 molecules. On the other hand, maturation of tissues wrapped inside
 aluminium foil can sometimes be too open of a system, leading to loss of
 both labile and recalcitrant materials. Here we present a novel
 experimental procedure for maturing tissues under elevated
 pressure/temperature inside compacted sediment. In this procedure, porous
 sediment allows for labile maturation breakdown products to escape from
 the sample into the sediment and maturation chamber while recalcitrant,
 immobile components are contained, in a manner expected to be similar to
 the natural conditions of fossilisation. To test the efficacy of this
 novel procedure with respect to simulating fossil diagenesis in a simple
 case study, we investigate the differential survival of melanosomes
 relative to proteinaceous tissues through maturation of fresh lizard body
 parts and feathers. Macro- and ultrastructures are then compared to
 fossils. Similar to many carbonaceous exceptional fossils, the resulting
 organic components are thin, dark films composed mainly of exposed
 melanosomes resting on the sediment in association darkened bones.
 Keratinous, muscle, collagenous, and adipose tissues appear to be lost.
 Such results are consistent with predictions derived from
 non-sediment-encased maturation experiments and our understanding of
 biomolecular stability. These experiments might also suggest that organic
 preservation is largely driven by the original molecular composition of
 the tissue and the diagenetic stability of those molecules, rather than
 the tissue’s decay resistance alone, and this should be experimentally
 explored in the future.
description: Supporting
 Material
DOI: 10.5061/dryad.vp86v3r0
title: Data from: Patterns of primary succession of native and introduced plants in lowland wet forests in eastern Hawai‘i

description: The majority of Hawaii’s lowland wet forests no longer exist, with many of
 the last remaining patches found on the eastern, windward sides of the
 largest islands. To better understand successional patterns and invasion
 in these native systems, we quantified basal area (BA) and densities of
 woody species and understory cover at nine sites in the Puna district on
 the Island of Hawai‘i, representing age gradients of native stand
 development on both ‘a’ā and pāhoehoe lava flows. On both flow types, BA
 of native species increased (from 5 to 50 m2/ha) and stem densities
 decreased (from 3700 to 2600 stems/ha) with increasing stand/flow age.
 Both native and introduced species compositions diverged between substrate
 types on older flows. We found that lowland wet native forests remain at
 least partially intact in several locations, but their functional and
 compositional integrity is increasingly compromised by invasion of
 nonnative species, such as Psidium cattleianum and Melastoma candidum,
 which become more common at sites greater than 300-yr old. This time
 period may represent a threshold, after which abiotic environmental
 conditions no longer constrain recruitment of introduced species. On older
 flows, nonnative stem densities swamped those of native species by an
 order of magnitude, with nonnative stems (height &gt; 1.3 m) achieving
 densities as high as 18,000 stems/ha. In addition, all stands lacked
 recruitment of native woody species in the understory, suggesting that
 without management, the native components of these forests may soon no
 longer be self-sustaining.
description: lowland_wetforest_survey_200308_9sites_QA200601_NZCSV file with raw species counts and IDs as described in the publication.
DOI: 10.5061/dryad.s2nr5
title: Data from: Feeding evolution of a herbivore influences an arthropod community through plants: implications for plant-mediated eco-evolutionary feedback loop

description: 1. Genetic variation in individual species can have important ecological
 consequences, and sometimes, these interactions are mediated through
 another species. For example, genetic variation in an herbivore could
 alter plant responses that then influence other plant-associated
 arthropods. However, few systems have experimentally tested the ecological
 consequences of genetic variation as mediated through other species,
 especially within the same trophic community context. 2. I studied how
 evolution of feeding preference in the willow leaf beetle (Plagiodera
 versicolora), which occurs under selection in a herbivore community
 context, feeds back to an arthropod community through plant-mediated
 indirect interactions. Previous studies show beetle populations locally
 adapt distinct preferences ranging from the gourmet-type, which feeds
 exclusively on new leaves of willows, to the no-preference (no-pref) type,
 which displays non-preferential feeding on leaves of different ages. 3. I
 conducted field experiments at two sites that mimicked evolutionary
 changes in the feeding preference of the leaf beetle. I manipulated the
 composition of leaf beetle feeding types for 6 days in spring and then
 investigated subsequent development of arthropod communities. I found that
 initial herbivory by a higher proportion of gourmet-type beetles led to
 lower subsequent abundance of conspecific beetle larvae. In contrast, a
 higher proportion of gourmet-type beetles resulted in higher abundance of
 aphids. Aphid-tending ants also increased with the increasing abundance of
 aphids. As a result, species diversity of arthropod communities decreased
 with the proportion of gourmet-type beetles in the initial beetle
 treatment. 4. Community assembly dynamics were significantly influenced by
 interactive effects between the initial beetle treatment and subsequent
 colonizer species identities. Thus, beetle genetic variation had
 long-lasting effects through a temporal chain of indirect interactions
 likely mediated through induced plant responses and the abundance of
 aphids. 5. Synthesis. Evolutionary changes in feeding traits within an
 herbivore species had profound but predictable impact on local arthropod
 communities. Because the feeding evolution of herbivores nearly always
 occurs in a community context, plant-mediated feedback loops between the
 evolution and ecological community of arthropods may be widespread in
 nature.
description: Data_EcoEvo_JEcol_utmData on arthropod communities, herbivory, and plant traits colleted from experiments. Please see the article for details on the treatment and experimental design.
DOI: 10.5061/dryad.sn878
title: Data from: Horizontal hostility among non-meat eaters

description: The present study examined intergroup judgments made between four groups
 of non-meat eaters: health vegetarians; ethical vegetarians; health
 vegans, and ethical vegans. Consistent with hypotheses based on horizontal
 hostility and the need to maintain ingroup distinctiveness, ethical
 vegetarians gave unfavorable evaluations to health vegetarians relative to
 vegans, especially when the mainstream omnivore group was made salient.
 Contrary to expectations, vegans gave relatively more favorable
 evaluations to ethical vegetarians than health vegetarians when mainstream
 salience was low. This was especially true for vegans who were motivated
 primarily by ethical concerns. When mainstream salience was high, vegans
 did not distinguish between the vegetarian subgroups. Results suggest that
 one’s motives for abstaining from meat often play a larger role in this
 type of intergroup perceptions than one’s dietary practices.
description: hhspss
 file
DOI: 10.5061/dryad.86088n1
title: Data from: Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs

description: Neuropsychiatric disorders are the third leading cause of global disease
 burden. Current pharmacological treatment for these disorders is
 inadequate, with often insufficient efficacy and undesirable side effects.
 One reason for this is that the links between molecular drug action and
 neurobehavioral drug effects are elusive. We use a big data approach from
 the neurotransmitter response patterns of 258 different neuropsychiatric
 drugs in rats to address this question. Data from experiments comprising
 110,674 rats are presented in the Syphad database [www.syphad.org].
 Chemoinformatics analyses of the neurotransmitter responses suggest a
 mismatch between the current classification of neuropsychiatric drugs and
 spatiotemporal neurostransmitter response patterns at the systems level.
 In contrast, predicted drug–target interactions reflect more appropriately
 brain region related neurotransmitter response. In conclusion the
 neurobiological mechanism of neuropsychiatric drugs are not well reflected
 by their current classification or their chemical similarity, but can be
 better captured by molecular drug–target interactions.
description: Supplementary_Data_NooriDownloadable version of syphad database
DOI: 10.5061/dryad.t04k1
title: Data from: A down-shifting Eu 3+ -doped Y 2 WO 6 /TiO 2 photoelectrode for improved light harvesting in dye-sensitized solar cells

description: Y1.86Eu0.14WO6 phosphors were prepared using a solid-state reaction
 method. Their optical properties were analysed, and they was mixed with
 TiO2, sintered, and used as a photoelectrode (PE) in dye-sensitized solar
 cells (DSSCs). The as-prepared photoelectrode was characterized by
 photoluminescence spectroscopy, diffuse reflectance, electrochemical
 impedance spectroscopy (EIS) and X-ray diffraction. The photoelectric
 conversion efficiency of the DSSC with TiO2:Y1.86Eu0.14WO6 (100:2.5) was
 25.8% higher than that of a DSCC using pure TiO2 as PE. This high
 efficiency is due to the ability of the luminescent material to convert
 ultraviolet radiation from the sun to visible radiation, thus improving
 the solar light harvesting of the DSSC.
description: Materials and General
 MethodsA general description of
 the methods and materials used for prepare the photoelectrode and the dye
 sensitized solar cell as well.Fig. 2Data sheet Fig
 2Fig. 3Data sheet Fig
 3Fig. 4Data sheet Fig.
 4Fig5.Data sheet Fig.
 5Fig. 6data sheet Fig.
 6Fig. 7Data sheet Fig.
 7Fig. 8Data sheet Fig.
 8
DOI: 10.5061/dryad.h9873
title: Data from: Do habitat shifts drive the diversity in teleost fishes? An example from the pufferfishes (Tetraodontidae)

description: Habitat shifts are implicated as the cause of many vertebrate radiations,
 yet relatively few empirical studies quantify patterns of diversification
 following colonization of new habitats in fishes. The pufferfishes (family
 Tetraodontidae) occur in several habitats, including coral reefs and
 freshwater, which are thought to provide ecological opportunity for
 adaptive radiation, and thus provide a unique system for testing the
 hypothesis that shifts to new habitats alter diversification rates. To
 test this hypothesis we sequenced eight genes for 96 species of
 pufferfishes and closely related porcupine fishes, and added 19 species
 from sequences available in GenBank. We time-calibrated the molecular
 phylogeny using three fossils, and performed several comparative analyses
 to test whether colonization of novel habitats led to shifts in the rate
 of speciation and body size evolution, central predictions of clades
 experiencing ecological adaptive radiation.. Colonization of freshwater is
 associated with lower rates of cladogenesis in pufferfishes though these
 lineages also exhibit accelerated rates of body size evolution. Increased
 rates of cladogenesis are associated with transitions to coral reefs, but
 reef lineages surprisingly exhibit significantly lower rates of body size
 evolution. These results suggest that ecological opportunity afforded by
 novel habitats may be limited for pufferfishes due to competition with
 other species, constraints relating to pufferfish life history and trophic
 ecology, and other factors.
description: Santini_et_al_2013_timetreePufferfish timetree, Newick formatSantini_et_al_2013_115taxa_8genesPufferfish DNA alignment, Nexus format
DOI: 10.5061/dryad.ns905
title: Data from: Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations

description: Current conservation practices exclude human-generated hybridized
 populations from protection, as the genetic effects of hybridization in
 the wild have been observed to be long-lasting based on neutral genetic
 markers and are considered potentially irreversible. Theory, however,
 predicts otherwise for genes under selection. We transplanted combinations
 of wild, domesticated and hybridized populations of a fish species to new
 environments. We then compared survival, phenotypic variation and
 plasticity to determine whether hybridization affects adaptive potential
 after multiple generations of selection in the wild. Although the fitness
 of our hybridized populations at the onset of hybridization cannot be
 assessed, our results suggest that within five to eleven generations,
 selection can remove introduced foreign genes from wild populations that
 have hybridized with domesticated conspecifics. The end result is
 hybridized populations that, in terms of survival, phenotypic plasticity,
 mean trait expression and overall general responses to environmental
 change, closely resemble neighbouring wild populations. These results have
 important implications for considering the potential conservation value of
 hybridized populations and illustrate the effectiveness of selection in a
 local environment.
description: Data from a transplant
 experiment involving hybridized and non-hybridized populations of brook
 troutThis data file contains
 field, genetic and morphological data from a transplant experiment in
 which brook trout from two hybridized (Welcome and Charles Lakes), one
 non-hybridized (Dickson Lake) and one hatchery population (Hills Lake
 strain) were match planted into three experimental study lakes. A 5th
 population (Shallnot Lake) is included in the data but was not included in
 the publication due to its uncertain genetic
 background.Data for
 Dryad.xlsx