cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wpzgmsbhg
title: Changes in tree community structures in defaunated forests are not driven only by dispersal limitation

description: 1. Bushmeat hunting has reduced population sizes of large frugivorous
 vertebrates throughout the tropics, thereby reducing the dispersal of
 seeds. This is believed to affect tree population dynamics, and therefore
 community composition, because the seed dispersal of large-seeded trees
 depends upon large-bodied vertebrates. 2. We report on a long-running
 study of the effect of defaunation on a tropical tree community. In three
 censuses over 11 years, we compared sapling recruitment between a hunted
 and a nonhunted site, which are nearby and comparable to one another, to
 determine the extent to which species composition has changed through time
 following defaunation. We expected to find a reduced abundance of tree
 species that rely on large frugivores for dispersal at the hunted site,
 and altered community structure as a consequence. 3. Although community
 composition at the hunted site diverged from that at the nonhunted site,
 the changes were independent of dispersal syndrome, with no trend towards
 a decline in species that are dispersed by large, hunted vertebrates.
 Moreover, the loss of large-bodied dispersers did not generate the changes
 in tree community composition that we hypothesised. Some species presumed
 to rely on large-bodied frugivores for dispersal are effectively
 recruiting despite the absence of their dispersers. 4. Synthesis: The
 presumption that forests depleted of large-bodied dispersers will
 experience rapid, directional compositional change is not fully supported
 by our results. Altered species composition in the sapling layer at the
 hunted site, however, indicates that defaunation may be connected with
 changes to the tree community, but that the nature of these changes are
 not unidirectional as previously assumed. It remains difficult to predict
 how defaunation will affect tree community composition without a deeper
 understanding of the driving mechanisms at play.
description: Data was collected between 2004 and 2015 from a hunted site (Boca
 Manu) and a non-hunted site (Cocha Cashu). Tree plots covered one 4-ha
 plot at each site, with a central square 1- or 1.08-ha sapling plot at the
 hunted and nonhunted sites, respectively. In each census, every individual
 was identified, tagged and mapped, DBH was measured for trees (≥10 cm DBH)
 and large saplings (&gt;1 cm DBH, &lt;10 cm DBH), and height was
 measured for smaller saplings (&gt;1 m height, &lt;1 cm
 DBH). Four data sets are provided, two for mature trees
 at each site and two for saplings at each site.
description: Metadata tabs provides detailed information on columns. Data may
 be missing if tree measurements were not obtained in unusual
 circumstances. If the tree was dead or not yet recruited into the study no
 height or DBH measurements are provided.
DOI: 10.5061/dryad.d2547d804
title: Timescales of motor memory formation in dual-adaptation

description: The timescales of adaptation to novel dynamics are well explained by a
 dual-rate model with slow and fast states. This model can predict
 interference, savings and spontaneous recovery, but cannot account for
 adaptation to multiple tasks, as each new task drives unlearning of the
 previously learned task. Nevertheless, in the presence of appropriate
 contextual cues, humans are able to adapt simultaneously to opposing
 dynamics. Consequently this model was expanded, suggesting that
 dual-adaptation occurs through a single fast process and multiple slow
 processes. However, such a model does not predict spontaneous recovery
 within dual-adaptation. Here we assess the existence of multiple fast
 processes by examining the presence of spontaneous recovery in two
 experimental variations of an A-B-Error-clamp paradigm within dual-task
 adaptation in humans. In both experiments, evidence for spontaneous
 recovery towards the initially learned dynamics (A) was found in the
 error-clamp phase, invalidating the one-fast-two-slow dual-rate model.
 However, as adaptation is not only constrained to two timescales, we fit
 twelve multi-rate models to the experimental data. BIC model comparison
 again supported the existence of two fast processes, but extended the
 timescales to include a third rate: the ultraslow process. Overall, we
 show that dual-adaptation can be best explained by a two-fast-triple-rate
 model over the timescales of adaptation studied here. Longer term learning
 may require even slower timescales, explaining why we never forget how to
 ride a bicycle. Indeed, even within our single day experiment, we found
 little evidence for decay of the learned memory over several hundred
 error-clamp trials.
description: Usage notes included in Readme file with data
DOI: 10.5061/dryad.k98sf7m3f
title: Influence of density and salinity on larval development of salt-adapted and salt-naïve frog populations

description: Environmental change and habitat fragmentation will affect population
 densities for many species. For those species that have locally adapted to
 persist in changed or stressful habitats, it is uncertain how density
 dependence will affect adaptive responses. Anurans (frogs and toads) are
 typically freshwater organisms, but some coastal populations of green
 treefrogs (Hyla cinerea) have adapted to brackish, coastal wetlands.
 Tadpoles from coastal populations metamorphose sooner and demonstrate
 faster growth rates than inland populations when reared solitarily.
 Although saltwater exposure has adaptively reduced the duration of the
 larval period for coastal populations, increases in densities during
 larval development typically increase time to metamorphosis and
 reduce rates of growth and survival. We test how combined stressors of
 density and salinity affect larval development between salt-adapted
 (“coastal”) and non-salt adapted (“inland”) populations by measuring
 various developmental and metamorphic phenotypes. We found that increased
 tadpole density strongly affected coastal and inland tadpole populations
 similarly. In high-density treatments, both coastal and inland populations
 had reduced growth rates, greater exponential decay of growth, a smaller
 size at metamorphosis, took longer to reach metamorphosis, and had lower
 survivorship at metamorphosis. Salinity only exaggerated the effects of
 density on the time to reach metamorphosis and exponential decay of
 growth. Location of origin affected length at metamorphosis, with coastal
 tadpoles metamorphosing slightly longer than inland tadpoles across
 densities and salinities. These findings confirm that density has a strong
 and central influence on larval development even across divergent
 populations and habitat types and may mitigate the expression (and
 therefore detection) of locally adapted phenotypes.
DOI: 10.5061/dryad.m905qftxg
title: Stable resource polymorphism along the benthic littoral-pelagic axis in an invasive crayfish

description: Although intraspecific variability is
 now widely recognized
 as affecting evolutionary and ecological
 processes, our knowledge on the importance of intraspecific
 variability within invasive species is still limited. This
 is despite the fact that quantifying the extent
 of within-population morphological
 divergences associated with the use
 of different trophic or spatial resources (i.e.
 resource polymorphism) can help to better
 predict their ecological impacts on
 recipient ecosystems. Here, we quantified the
 extent of resource polymorphism within
 populations of a highly invasive
 species, Procambarus clarkii, in 16 lake
 populations by comparing their trophic (estimated
 using stable isotope analyses) and morphological characteristics
 between individuals from the littoral and pelagic habitats. Our
 results first demonstrated that crayfish occur
 in both littoral and pelagic habitats of 7
 lakes and that the use of pelagic habitat was associated
 with increased abundance of
 crayfish in the littoral
 habitat. We then found that individuals from
 littoral and pelagic
 habitats displayed significantly different body and chelae morphology and origin of resource use (i.e. reliance on littoral carbon). These results demonstrate the existence of resource polymorphism in invasive populations. There was no genetic differentiation between individuals from the two habitats, implying that this resource polymorphism was stable (i.e. high gene flow between individuals). Finally, we demonstrated that a divergent adaptive process was responsible for the morphological divergence in body and chela shapes btween habitats while difference in origin of the resource use neutrally evolved under genetic drift. These findings demonstrated that invasive P. clarkii can display strong within-population phenotypic variability in recent populations, and this could lead to contrasted ecological impacts between littoral and pelagic individuals.
DOI: 10.5061/dryad.ttdz08ktj
title: Reductions in the dietary niche of southern sea otters (Enhydra lutris nereis) from the Holocene to the Anthropocene.

description: The sea otter (Enhydra lutris) is a marine mammal hunted to near
 extinction during the 1800s. Despite their well-known importance as a
 keystone species, we know little about historical sea otter ecology. Here,
 we characterize the ecological niche of ancient southern sea otters (E.
 lutris nereis) using d13C and d15N analysis of bones recovered
 from archaeological sites spanning ~7,000 to 350 years before present
 (N=112 individuals) at five regions along the coast of California. These
 data are compared with previously published data on modern animals (N=165)
 and potential modern prey items. In addition, we analyze the d15N
 of individual amino acids for 23 individuals to test for differences in
 sea otter trophic ecology through time. After correcting for
 tissue-specific and temporal isotopic effects, we employ nonparametric
 statistics and Bayesian niche models to quantify differences among ancient
 and modern animals. We find ancient otters occupied a larger
 isotopic niche than nearly all modern localities; this likely reflects
 broader habitat and prey use in pre-fur trade populations. In addition,
 ancient sea otters at the most southerly ­sites occupied an isotopic niche
 that was more than twice as large as ancient otters from northerly
 regions. The latter likely reflects greater invertebrate prey diversity in
 southern California relative to northern California. Thus, we suggest the
 potential dietary niche of sea otters in southern California could be
 larger than in central and northern California. At two sites, Año Nuevo
 and Monterey Bay, ancient otters had significantly higher d15N
 values than modern populations. Amino acid d15N data indicated
 this resulted from shifting baseline isotope values, rather than a change
 in sea otter trophic ecology. Our results help in better understanding the
 contemporary ecological role of sea otters and exemplify the strength of
 combing zooarchaeological and biological information to provide baseline
 data for conservation efforts.
description: LIST OF SUPPLEMENTARY DATA
 TABLES <b>Table S1.</b> Isotopic results of
 paired tissues from stranded sea otters in central California.
 <b>Table S2. </b>Ancient and modern sea otter
 samples. <b>Table S3.</b> ANOVA and Tukey’s
 HSD results for pairwise comparisons of sea otter bulk tissue
 d<sup>13</sup>C and d<sup> 15</sup>N
 values. <b>Table S4.</b> ANOVA and Tukey’s
 HSD results for pairwise comparisons of ancient and modern sea otter
 d<sup>13</sup>C and d<sup> 15</sup>N
 values.
DOI: 10.5061/dryad.xksn02vbs
title: Habitat complexity dampens selection on prey activity level

description: Conspecific prey individuals often exhibit persistent differences in
 behavior (i.e., animal personality) and consequently vary in their
 susceptibility to predation. How this form of selection varies across
 environmental contexts is essential to predicting ecological and
 evolutionary dynamics, yet remains currently unresolved. Here, we use
 three separate predator–prey systems (sea star–snail, wolf spider–cricket,
 and jumping spider–cricket) to independently examine how habitat
 structural complexity influences the selection that predators impose on
 prey behavioral types. Prior to conducting staged predator–prey
 interaction encounters, we ran prey individuals through multiple
 behavioral assays to determine their average activity level. We then
 allowed individual predators to interact with groups of prey in either
 open or structurally complex habitats and recorded the number and
 individual identity of prey that were eaten. Habitat complexity had no
 effect on overall predation rates in any of the three predator–prey
 systems. Despite this, we detected a pervasive interaction between habitat
 structure and individual prey activity level in determining individual
 prey survival. In open habitats, all predators imposed strong selection on
 prey behavioral types: sea stars preferentially consumed sedentary snails,
 while spiders preferentially consumed active crickets. Habitat complexity
 dampened selection within all three systems, equalizing the predation risk
 that active and sedentary prey faced. These findings suggest a general
 effect of habitat complexity that reduces the importance of prey activity
 level in determining individual predation risk. We reason this occurs
 because activity level (i.e., movement) is paramount in determining risk
 within open environments, whereas in complex habitats, other behavioral
 traits (e.g., escape ability to a refuge) may take precedence.
DOI: 10.5061/dryad.m0cfxpp06
title: Generalist plants are more competitive and more functionally similar to each other than specialist plants: insights from network analyses

description: Aim: Ecological specialization is a property of species associated with
 the variety of contexts they occupy. Identifying the mechanisms
 influencing specialization is critical to understand species coexistence
 and biodiversity patterns. However, the functional attributes leading to
 specialization are still unknown. Similarly, there is contrasting evidence
 between the level of specialization and local abundance of species. We ask
 whether plant specialist and generalist species (i) are associated with
 distinct functional profiles, using core plant functional traits and
 strategies, (ii) show comparable functional variation, and how (iii) they
 perform at local scale. Location: France, Countrywide scale. Taxon:
 Herbaceous plants. Results: We identified five major modules in the
 bipartite network, related to different environmental conditions and
 composed of species displaying different functional attributes. Species
 that were more specialist were less competitive, had smaller stature,
 higher stress-tolerance and stronger resource conservation, while
 generalist species were taller. Generalists were also more similar among
 themselves than specialists. In addition, specialist species had higher
 local abundances and occurred in communities with plants of similar
 height. Main conclusions: We found distinctive functional signatures of
 specialist and generalist species in grassland communities across diverse
 environments at regional and community scales. Network metrics can benefit
 community ecology to test classical macro-ecological hypotheses by
 identifying distinct ecological unit at large scale and quantifying the
 links developed by species.
description: Our approach is based on the structure of a bipartite network
 integrating the occurrences of ~2.900 plant species in ~90.000 sites. We
 identified ecologically coherent sets of species and sites, called
 modules. To define a metrics of specialization, we quantified the
 occurrences of species in sites belonging to one or several modules. We
 used functional traits related to resource acquisition, competition for
 light, dispersal abilities and indices of competitive, stress-tolerance
 and ruderal strategies.
description: One file contains a site-species matrix filled with the relative
 abundances of species. The matrix contains 84199 communities,
 corresponding to the communities belonging to the five main modules. It
 has 2071 species. The data frame records for each of
 the 84199 communities the Community Weighted Mean values of the following
 functional traits: Specific Leaf Area (SLA), Plant Height (PH), Seed Mass
 (SM), Leaf Area (LA), Leaf Nitrogen Content (LNC) and Leaf Dry Matter
 Content (LDMC). The CWM calculated for the three CSR scores are also
 available. Finally, the module of each community is reported.
DOI: 10.7272/q66h4fm2
title: Data from: Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by PhIP-Seq

description: The identification of autoantigens remains a critical challenge for
 understanding and treating autoimmune diseases. Autoimmune polyendocrine
 syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as
 widespread autoimmunity with T and B cell responses to multiple organs.
 Importantly, autoantibody discovery in APS1 can illuminate fundamental
 disease pathogenesis, and many of the antigens found in APS1 extend to
 common autoimmune diseases. Here, we performed proteome-wide programmable
 phage-display (PhIP-Seq) on sera from an APS1 cohort and discovered
 multiple common antibody targets. These novel autoantigens exhibit
 tissue-restricted expression, including expression in enteroendocrine
 cells and dental enamel. Using detailed clinical phenotyping, we find
 novel associations between autoantibodies and organ-restricted
 autoimmunity, including between anti-KHDC3L autoantibodies and premature
 ovarian insufficiency, and between anti-RFX6 autoantibodies and
 diarrheal-type intestinal dysfunction. Our study highlights the utility of
 PhIP-Seq for interrogating antigenic repertoires in human autoimmunity and
 the importance of antigen discovery for improved understanding of disease
 mechanisms.
description: DNA libraries were barcoded and amplified, gel purified, and
 subjected to Next-Generation Sequencing on an Illumina MiSeq Instrument
 (Illumina, San Diego, CA). Sequencing reads from raw fastq files (see:
 <strong>fastq.gz files</strong>) were aligned to the reference
 oligonucleotide library (see:
 <strong>reference.fasta</strong>) using bowtie2. Peptide
 counts were subsequently normalized by converting raw reads to percentage
 of total reads per sample (see: <strong>peptides.csv;
 </strong>for peptide sequences and gene conversion, see:
 <strong>peptides_seq_gene.csv</strong>). Peptide counts were
 also summed across all fragments mapping to the same gene for gene-level
 counts (see: <strong>genes.csv</strong>). Peptide and
 gene-level enrichments for both APS1 and non-APS1 sera were calculated by
 determining the fold-change of read percentage per peptide and gene in
 each sample over the mean read percentage per peptide and gene in a
 background of mock-IP.
DOI: 10.5061/dryad.fn2z34tqd
title: Data from: Acute cytotoxicity and increased vascular endothelial growth factor after in vitro nitrogen mustard vapor exposure

description: RATIONALE:  Nitrogen mustard (NM) is a highly toxic alkylating
 agent.  It is classified as chemical threat due to its potential
 use as a warfare agent.  When inhaled, mustard exposure can cause
 both acute and chronic lung injury.  The aims of this study are
 to develop an in vitro culture system for modeling mustard-induced airway
 injury and to identify growth factors contributing to airway pathology.
 METHODS:  Primary human bronchial epithelial cells co-cultured
 with primary human pulmonary endothelial cells were exposed to NM (25, 50,
 100, 250 or 500 µM) or PBS (control) for 1 hour.  Lactate
 dehydrogenase (LDH) and trans-epithelial electrical resistance (TEER) were
 measured prior to and 24 hours after NM exposure.  Endothelial
 cultures were then stained for live/dead staining.  Exposed
 airway media was also analyzed for growth factors using Luminex multiplex
 technology.  RESULTS:  A one-hour NM vapor exposure
 increased supernatant LDH and decreased TEER at 24 hours for all cultures
 exposed to NM concentrations greater than or equal to 50 µM. 
 Evidence of endothelial cell death occurred at NM concentrations of 250
 and 500 µM. Vascular endothelial growth factor (VEGF) signaling,
 specifically VEGF-A and placental growth factor (PlGF), increased in
 NM-exposed co-culture media compared to PBS
 controls.    CONCLUSIONS:  NM vapor
 exposure causes significant airway epithelial and endothelial
 injury.  Increased VEGF signaling occurred in airway co-cultures
 exposed to higher NM concentrations with concurrent endothelial cell
 death.  Future studies are required to validate the role of VEGF
 signaling in both acute and chronic mustard-induced airway
 pathology.
DOI: 10.5061/dryad.b2rbnzs9p
title: Evolution and development at the origin of a phylum

description: Quantifying morphological evolution is key to determining the patterns and
 processes underlying the origin of phyla. We constructed a hierarchical
 morphological character matrix to characterize the radiation and
 establishment of echinoderm body plans during the early Paleozoic. This
 showed that subphylum-level clades diverged gradually through the
 Cambrian, and the distinctiveness of the resulting body plans was
 amplified by the extinction of transitional forms and obscured by
 convergent evolution during the Ordovician. Higher-order characters that
 define these body plans were not fixed at the origin of the phylum,
 countering hypotheses regarding developmental processes governing the
 early evolution of animals. Instead, these burdened characters were
 flexible enabling continued evolutionary innovation throughout the clades’
 history.
description: We constructed a novel character matrix comprising 413 characters
 incorporating the range of morphologies in early Paleozoic echinoderms .
 This character suite was constructed hierarchically and attempted to avoid
 overt phylogenetic signal by including autapomorphies and obviously
 homoplastic characters. This character suite was used to code 366 early
 Paleozoic echinoderm genera, including a nearly comprehensive sampling of
 Cambrian and Ordovician echinoderms along with representatives from groups
 in which definitive articulated body fossils are first recorded from the
 middle Paleozoic (Dataset S1). In addition, this
 dataset was recoded based on an alternative interpretation of homoalozoan
 morphology (Dataset S2).  Scripts are included for
 reconstructing ancestral character states and constructing a theorectical
 morphospace.