cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pk0p2ngkz
title: Timing and impact of psychiatric, cognitive and motor abnormalities in Huntington disease: Supplemental information

description: Objective To assess the prevalence, timing and functional impact of
 psychiatric, cognitive and motor abnormalities in Huntington’s disease
 (HD) gene carriers, we analysed retrospective clinical data from
 individuals with manifest HD. Methods Clinical features of HD patients
 were analysed for 6316 individuals in the European REGISTRY study from 161
 sites across 17 countries.  Data came from clinical
 history and the patient-completed Clinical Characteristics Questionnaire
 that assessed eight symptoms: motor, cognitive, apathy, depression,
 perseverative/obsessive behavior, irritability, violent/aggressive
 behavior, and psychosis. Multiple logistic regression was used to analyse
 relationships between symptoms and functional outcomes. Results The
 initial manifestation of HD is increasingly likely to be motor, and less
 likely to be psychiatric, as age at presentation increases, and is
 independent of pathogenic CAG repeat length. The Clinical Characteristics
 Questionnaire captures data on non-motor symptom prevalence that correlate
 specifically with validated clinical measures. Psychiatric and cognitive
 symptoms are common in HD gene carriers, with earlier onsets associated
 with longer CAG repeats. 42.4% of HD patients reported at least one
 psychiatric or cognitive symptom before motor symptoms, with depression
 most common. Each non-motor symptom was associated with significantly
 reduced total functional capacity scores. Conclusions Psychiatric and
 cognitive symptoms are common and functionally debilitating in HD gene
 carriers. They require recognition and targeting with clinical outcome
 measures and treatments. However, as it is impossible to distinguish
 confidently between non-motor symptoms arising from HD and primary
 psychiatric disorders, particularly in younger pre-manifest patients,
 non-motor symptoms should not be used to make a clinical diagnosis of HD.
description: The data used in this study were taken from the Europen
 Registry-HD study (http://www.euro-hd.net/html/REGISTRY; NCT01590589). Please see our manuscript for the full methodology used.
DOI: 10.5061/dryad.j0zpc86cd
title: Microgeographic divergence of functional responses among salamanders under antagonistic selection from apex predators

description: A predator's functional response determines predator–prey
 interactions by describing the relationship between the number of prey
 available and the number eaten. Its shape and parameters fundamentally
 govern the dynamic equilibrium of predator–prey interactions and their
 joint abundances. Yet, estimates of these key parameters generally assume
 stasis in space and time and ignore the potential for local adaptation to
 alter feeding responses and the stability of trophic dynamics. Here, we
 evaluate if functional responses diverge among populations of spotted
 salamander ( Ambystoma maculatum ) larvae that face antagonistic selection
 on feeding strategies based on their own risk of predation. Common garden
 experiments revealed that spotted salamander from ponds with varying
 predation risks differed in their functional responses, suggesting an
 evolutionary response. Applying mechanistic equations, we discovered that
 the combined changes in attack rates, handling times and shape of the
 functional response enhanced feeding rate in environments with high
 densities of gape-limited predators. We suggest how these parameter
 changes could alter community equilibria and other emergent properties of
 food webs. Community ecologists might often need to consider how local
 evolution at fine scales alters key relationships in ways that alter local
 diversity patterns, food web dynamics, resource gradients and community
 responses to disturbance.
description: We evaluated prey eaten versus prey given in larvae raised in a
 common garden experiment from different populations.
description: Column names: rep - temporal replicate; pred.risk - high or low
 marbled salamander predation risk in natal pond; cue - with or without
 chemical cues from marbled salamanders (AMOP); vase - container number;
 family - sibship number (egg mass); food.given - number of Daphnia
 provided initially; food.eaten - number of Daphnia eaten after 24 hours;
 wt - larval wet mass in mg.
DOI: 10.5061/dryad.tx95x69w6
title: Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Background Parasitoidism, a specialized life strategy in which a parasite
 eventually kills its host, is frequently found within the insect order
 Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two
 dominant life strategies within the hymenopteran superfamily Cynipoidea,
 with the other being an unusual plant-feeding behavior known as galling.
 Less commonly cynipoid wasps exhibit inquilinism, a strategy where some
 species have adapted to usurp other species’ galls instead of inducing
 their own. Using a phylogenomic data set of ultraconserved elements from
 nearly all lineages of Cynipoidea, we here generate a robust phylogenetic
 framework and timescale to understand cynipoid systematics and the
 evolution of these life histories. Results Our reconstructed evolutionary
 history for Cynipoidea differs considerably from previous hypotheses.
 Rooting our analyses with non-cynipoid outgroups, the Paralaucini, a group
 of inquilines, emerged as sister-group to the rest of Cynipoidea,
 rendering the gall wasp family Cynipidae paraphyletic. The families
 Ibaliidae and Liopteridae, long considered archaic and early-branching
 parasitoid lineages, were found nested well within the Cynipoidea as
 sister-group to the parasitoid Figitidae. Cynipoidea originated in the
 early Jurassic around 190 Ma. Either inquilinism or parasitoidism is
 suggested as the ancestral and dominant strategy throughout the early
 evolution of cynipoids, depending on whether a simple (three states:
 parasitoidism, inquilinism and galling) or more complex (seven states:
 parasitoidism, inquilinism and galling split by host use) model is
 employed. Conclusions Our study has significant impact on understanding
 cynipoid evolution and highlights the importance of adequate outgroup
 sampling. We discuss the evolutionary timescale of the superfamily in
 relation to their insect hosts and host plants, and outline how
 phytophagous galling behavior may have evolved from entomophagous,
 parasitoid cynipoids. We hypothesize these seemingly diverging life
 strategies may be considered as specializations of a similar underlying
 molecular toolkit between which switches are possible. Our study has
 established the framework for further physiological and comparative
 genomic work between gall-making, inquiline and parasitoid lineages, which
 could also have significant implications for the evolution of diverse life
 histories in other Hymenoptera.
DOI: 10.5061/dryad.rjdfn2z8k
title: Data for: Relative abundance of nitrogen cycling microbes in coral holobionts reflects environmental nitrate availability

description: Recent research suggests that nitrogen (N) cycling microbes are important
 for coral holobiont functioning. In particular, coral holobionts may
 acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove
 excess N via denitrification activity. However, our understanding of
 environmental drivers on these processes in
 hospite remains limited. Employing the strong seasonality of the
 central Red Sea, this study assessed the effects of environmental
 parameters on the proportional abundances of N cycling microbes associated
 with the hard corals Acropora
 hemprichii and Stylophora
 pistillata. Specifically, we quantified changes in the relative
 ratio between nirS and nifH gene copy
 numbers, as a proxy for seasonal shifts in denitrification and
 N2 fixation potential in corals, respectively. In addition, we
 assessed coral tissue-associated Symbiodiniaceae cell densities and
 monitored environmental parameters to provide a holobiont and
 environmental context, respectively. While ratios
 of nirS to nifH gene copy numbers
 varied between seasons, they revealed similar seasonal patterns in both
 coral species, with ratios closely following patterns in environmental
 nitrate availability. Symbiodiniaceae cell densities aligned with
 environmental nitrate availability, suggesting that the seasonal shifts
 in nirS to nifH gene abundance ratios
 were probably driven by nitrate availability in the coral holobiont.
 Thereby, our results suggest that N cycling in coral holobionts probably
 adjusts to environmental conditions by increasing and/or decreasing
 denitrification and N2 fixation potential according to
 environmental nitrate availability. Microbial N cycling may, thus,
 extenuate the effects of changes in environmental nitrate availability on
 coral holobionts to support the maintenance of the coral–Symbiodiniaceae
 symbiosis.
DOI: 10.5061/dryad.tmpg4f4x3
title: Supplementary references from: Thrombus composition, imaging, and outcome prediction in acute ischemic stroke

description: Purpose of the Review: This article reviews the biochemical,
 structural, and imaging characteristics of intracranial thrombi in acute
 ischemic stroke; the relationship between thrombus composition and
 response to lytic and endovascular therapies; and current and future
 directions for improving outcomes in acute stroke patients based on
 thrombus characteristics. Recent Findings: New imaging techniques have
 advanced our ability to capture thrombus characteristics and burden in
 real-time, An improved understanding of recanalization rates with
 thrombolysis and endovascular thrombectomy based on thrombi has spurred
 interest in new acute therapies for acute stroke. Summary: Thrombus
 composition, size, location, and timing from stroke onset correlate with
 imaging findings in acute ischemic stroke and are associated with clinical
 outcome. Further research across multiple domains could assist in
 better applying our knowledge of thrombi to patient selection and
 individualization of acute therapies.
DOI: 10.5061/dryad.6m905qfz3
title: Female ornaments: is red skin color attractive to males and related to condition in rhesus macaques?

description: Sexual selection produces extravagant male traits, such as colorful
 ornaments, via female mate choice. More rarely, in mating systems in which
 males allocate mating effort between multiple females, female ornaments
 may evolve via male mate choice. Females of many anthropoid primates
 exhibit ornaments that indicate intra-individual cyclical fertility, but
 which have also been proposed to function as inter-individual quality
 signals. Rhesus macaque females are one such species, exhibiting cyclical
 facial color variation that indicates ovulatory status, but in which the
 function of inter-individual variation is unknown. We collected digital
 images of the faces of 32 rhesus macaque adult females. We assessed mating
 rates, and consortship by males, according to female face coloration. We
 also assessed whether female coloration was linked to physical (skinfold
 fat, BMI) or physiological (fecal glucocorticoid metabolite fGCM, urinary
 C-peptide concentrations) condition. We found that redder-faced females
 were mated more frequently, and consorted for longer periods by top-ranked
 males. Redder females had higher fGCM concentrations, perhaps related to
 their increased mating activity and consequent energy mobilization, and
 blood-flow. Prior analyses have shown that female facial redness is a
 heritable trait, and that redder-faced females have higher annual
 fecundity, while other evidence suggests that color expression is likely
 to be a signal rather than a cue. Collectively, the available evidence
 suggests that female coloration has evolved at least in part via male mate
 choice. Its evolution as a sexually-selected ornament attractive to males
 is probably attributable to the high female reproductive synchrony found
 in this species.
description: Higham-et-al-2020-rhesus-female-color-daily-data.csv - daily
 measures of female color (Red = RGB and DARK = luminance), fGCM (fecal
 glucocorticoid metabolites), UCP (urinary c-peptides), and behavior
 (whether a female was consorted by a top male or not, and the number of
 mating series in which she was involved), plus dominance ranks for each
 female
 Higham-et-al-2020-rhesus-female-color-averaged-values.csv - color
 measures averaged over the mating season per female (Red = RGB and DARK =
 luminance), plus BMI (body mass index, kg/m<sup>2</sup>) and
 skinfold fat measurements, plus dominance ranks for each female
 Higham-et-al-2020-rhesus-female-color-UCP-collection-times.csv -
 collection times for UCP data See the READ ME file for
 more details.
DOI: 10.5061/dryad.sf7m0cg4c
title: Competition as a demolition derby: Why tolerating competitors is more important than suppressing them

description: Tolerance and suppression are distinct components of competition among
 plants, and recognizing how they affect competitive outcomes is important
 for understanding the mechanisms and consequences of competition. We used
 simulations informed by experimental trials to ask whether tolerance or
 suppression of competitors was more important for the survival of native
 plants experiencing competition with an exotic invasive species. When
 competition was pairwise, tolerance and suppression contributed equally to
 competitive rank in simulations. However, when multiple native genotypes
 competed together against an invader, the ability to tolerate competition
 was up to 50 times more important than the ability to suppress the
 invader. In two-competitor communities the chief advantage of suppressing
 competitors was a global decrease in their abundance, but this advantage
 did not exist in communities of multiple competitors—which is more
 representative of natural conditions —because decreased competitor
 abundance benefited all plants regardless of their competitive ability. We
 suggest that this concept is analogous to a ‘demolition derby,’ an
 automotive contest where participants attempt to have the last functional
 vehicle on the playing field. Because strong suppressors share the
 benefits of eliminating competitors with other remaining competitors, we
 propose that tolerance of competitors is more beneficial than suppression
 when competition occurs in a multiplayer scenario—in a demolition derby
 and in nature. This finding has implications for our understanding of how
 competition influences plant species coexistence, plant community
 structure, and invasion outcomes.
description: Please see readme.
DOI: 10.5061/dryad.95x69p8j2
title: New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America

description: Taxa with broad geographic ranges that occur in different biomes and
 exhibit plastic morphological traits and/or adaptations to particular
 habitats make inferences about species boundaries especially challenging.
 However, technological and conceptual advances in the generation and
 analysis of genomic data have advanced the description of biodiversity.
 Here we address the outstanding questions about the delimitation of
 species in the genus Holochilus, a rodent with
 morphological specializations to wetland habitats, distributed through
 almost all the South America continent using genome‐wide SNP and
 morphometric data. Specifically, we apply a Bayesian model‐based species
 delimitation that revealed significant re-arrangements of species
 boundaries based on consideration of both morphometric and genomic data
 alone, or in combination. With these shifts in species boundaries, our
 results provide an insightful framework for inferring the group's
 biogeographic history and considering possible connections between
 disjoint biomes in South America. Because of the ecological constraints of
 the marsh rats, and with the proposed taxonomic re-arrangements, the
 significance of our findings extends beyond systematics and suggests how
 diversification might be associated with past ecological/environmental
 changes during the Pleistocene. Overall, this study highlights how genomic
 data can provide phylogenetic information for resolving relationships
 among species of Holochilus, but also the importance of
 integrative approaches to identify evolutionary independent species. For
 the relatively understudied vast wetlands of South America, a robust
 species delimitation framework therefore becomes a critical source of data
 relevant to hypotheses about the history of the biomes themselves.
DOI: 10.5061/dryad.hqbzkh1dr
title: Irisin directly stimulates osteoclastogenesis and bone resorption in vitro and in vivo: RNAseq dataset

description: Irisin, a skeletal-muscle secreted myokine, facilitates muscle-bone
 crosstalk and skeletal remodeling in part by its action on osteoblasts and
 osteocytes. In this study, we investigated whether irisin directly
 regulates osteoclasts. In vitro, irisin (2–10 ng/mL) increased osteoclast
 differentiation in C57BL/6J mouse bone marrow progenitors; however, this
 increase was blocked by a neutralizing antibody to integrin αVβ5. Irisin
 also increased bone resorption on several substrates in situ. RNAseq
 revealed differential gene expression induced by irisin including
 upregulation of markers for osteoclast differentiation and resorption, as
 well as osteoblast-stimulating ‘clastokines’. Forced expression of the
 irisin precursor Fndc5 in transgenic C57BL/6J mice resulted in lower bone
 mass at three ages and greater in vitro osteoclastogenesis from
 Fndc5-transgenic bone marrow progenitors. This study demonstrates that
 irisin acts directly on osteoclast progenitors to increase differentiation
 and promote bone resorption, supporting the tenet that irisin not only
 stimulates bone remodeling but may also be an important counter-regulatory
 hormone.
description: Total RNA was isolated with Trizol reagent and RNeasy mini
 kit from primary bone marrow progenitors induced to osteoclast
 differentiation with RANKL and MCSF, cultured with or without 10 ng/mL
 irisin for 7days. mRNA enrichment from 100 ng of total purified RNA and
 Illumina sequencing libraries preparation was performed using Kapa
 stranded mRNA Hyper Prep (Roche Sequencing Solutions, Pleasanton, CA,
 USA). Gene libraries were multiplexed in an equimolar pool and were
 sequenced on an Illumina NextSeq 500 with single-end 75 bp reads. Raw
 reads were aligned to the UCSC mm10 reference genome using a STAR
 aligner (version STAR_2.4.2a), and raw gene counts were quantified using
 the quantMode GeneCounts flag. Differential expression testing was
 performed using Limma and DESeq2. RNAseq analysis was performed using the
 VIPER snakemake pipeline. See linked manuscript for full
 details.
DOI: 10.5061/dryad.f7m0cfxth
title: Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity

description: CRISPR-Cas immune systems are widespread in bacteria and archaea, but not
 ubiquitous. Previous work has demonstrated that CRISPR immunity is
 associated with an infection-induced fitness cost, which may help explain
 the patchy distribution observed. However, the mechanistic basis of this
 cost has remained unclear. Using Pseudomonas
 aeruginosa PA14 and its phage DMS3vir as a model, we perform a
 30-day evolution experiment under phage mediated selection. We demonstrate
 that although CRISPR is initially selected for, bacteria carrying
 mutations in the phage receptor rapidly invade the population following
 subsequent reinfections. We then test three potential mechanisms for the
 observed cost of CRISPR: (1) autoimmunity from the acquisition of
 self-targeting spacers, (2) immunopathology or energetic costs from
 increased cas gene expression and (3) toxicity caused by
 phage gene expression prior to CRISPR-mediated cleavage. We find that
 phages can express genes before the immune system clears the infection and
 that expression of these genes can have a negative effect on host fitness.
 While infection does not lead to increased expression
 of cas genes, it does cause differential expression of
 multiple other host processes that may further contribute to the cost of
 CRISPR immunity. In contrast, we found little support for
 infection-induced autoimmunological and immunopathological effects. Phage
 gene expression prior to cleavage of the genome by the CRISPR-Cas immune
 system is therefore the most parsimonious explanation for the observed
 phage-induced fitness cost.
DOI: 10.5061/dryad.zgmsbcc8w
title: Digital biodiversity datasets reveal breeding phenology and its drivers in a widespread North American mammal

description: Shifts in reproductive timing are among the most commonly documented
 responses of organisms to global climate change. However, our knowledge of
 these responses is biased towards taxa that are easily observable and
 abundant in existing biodiversity data sets. Mammals are common subjects
 in reproductive biology, but mammalian phenology and its drivers in the
 wild remain poorly understood because many species are small, secretive,
 or labor-intensive to monitor. We took an informatics-based approach to
 reconstructing breeding phenology in the widespread North American deer
 mouse (Peromyscus maniculatus) using individual-level reproductive
 observations from digitized museum specimens and field censuses spanning
 &gt;100 years and &gt;45 degrees of latitude. We reconstructed
 female phenology in different regions and tested the importance of three
 environmental variables (photoperiod, temperature, precipitation) as
 breeding cues. Photoperiod and temperature were strong positive and
 negative breeding cues, respectively, while precipitation was not a
 significant predictor of breeding phenology. However, phenologies and the
 use of environmental cues varied substantially among regions, and we found
 evidence that these cueing repertoires are tuned to ecosystem-specific
 limiting conditions. Our results reiterate the importance of ecological
 context in optimizing reproduction and demonstrate how harmonization
 across biodiversity data resources allows new insight into phenology and
 its drivers in wild mammals.