cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wdbrv15k3
title: The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns

description: Due to its hemizygous inheritance and role in sex determination, the X
 chromosome is expected to play an important role in the evolution of
 sexual dimorphism, and to be enriched for sexually antagonistic genetic
 variation. By forcing the X chromosome to only be expressed in males over
 &gt;40 generations, we changed the selection pressures on the X to
 become similar to those experienced by the Y. This releases the X from any
 constraints arising from selection in females, and should lead to
 specialization for male fitness, which could occur either via direct
 effects of X-linked loci or trans-regulation of autosomal loci by the X.
 We found evidence of masculinization via upregulation of male-benefit
 sexually antagonistic genes, and downregulation of X-linked female benefit
 genes. Potential artifacts of the experimental evolution protocol are
 discussed and cannot be wholly discounted, leading to several caveats.
 Interestingly, we could detect evidence of microevolutionary changes
 consistent with previously documented macroevolutionary patterns, such as
 changes in expression consistent with previously established patterns of
 sexual dimorphism, an increase in the expression of metabolic genes
 related to mitonuclear conflict, and evidence that dosage compensation
 effects can be rapidly altered. These results confirm the importance of
 the X in the evolution of sexual dimorphism and as a source for sexually
 antagonistic genetic variation, and demonstrate that experimental
 evolution can be a fruitful method for testing theories of sex chromosome
 evolution.
description: See publication for details of experimental design and
 analysis. Population mean values (sheet 1) are
 calculated from vial mean values (sheet 2), which are in turn calculated
 from raw data (sheets 3 and 4). Relative fitness was
 standardized by sex by dividing by the mean value for each sex. Z-scores
 for fitness (used to improve fit to model assumptions) were obtained from
 the relative fitness values.
description: Missing values are denoted by NA.
DOI: 10.15468/dl.5wqbv5
title: Occurrence Download

description: A dataset containing 367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alysicarpus muelleri",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 367 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002266-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63xsj3v05
title: Positive selection and inactivation in vision and hearing genes of cetaceans

description: The transition to an aquatic lifestyle in cetaceans (whales and dolphins)
 resulted in a radical transformation in their sensory systems. Toothed
 whales acquired specialized high-frequency hearing tied to the evolution
 of echolocation, while baleen whales evolved low-frequency hearing. More
 generally, all cetaceans show adaptations for hearing and seeing
 underwater. To determine the extent to which these phenotypic changes have
 been driven by molecular adaptation, we performed large-scale targeted
 sequence capture of 179 sensory genes across the Cetacea, incorporating up
 to 54 cetacean species from all major clades as well as their closest
 relatives, the hippopotamuses. We screened for positive selection in 167
 loci related to vision and hearing, and found that the diversification of
 cetaceans has been accompanied by pervasive molecular adaptations in both
 sets of genes, including several loci implicated in non-syndromic hearing
 loss (NSHL). Despite these findings, however, we found no direct evidence
 of positive selection at the base of odontocetes coinciding with the
 origin of echolocation, as found in studies examining fewer taxa. By using
 contingency tables incorporating taxon- and gene-based controls, we show
 that, while numbers of positively selected hearing and NSHL genes are
 disproportionately high in cetaceans, counts of vision genes do not differ
 significantly from expected values. Alongside these adaptive changes, we
 find increased evidence of pseudogenization of genes involved in
 cone-mediated vision in mysticetes and deep diving odontocetes.
DOI: 10.5061/dryad.2jm63xskm
title: Data from: Soil microbes alter herbivore-induced volatile emissions in response to cereal cropping systems

description: Soil microbes can influence the emissions of plant volatile organic
 compounds (VOCs), which serve as host-location cues for insect pests and
 their natural enemies. Agricultural practices steer unique soil microbial
 communities, but how this influences crop VOCs and subsequent insect
 attraction remains unknown. The aim of this study was to investigate the
 effect of diversified agricultural practices on constitutive and
 herbivore-induced VOC emissions by crops through soil-microbe legacy
 effects. In a full factorial experiment, we measured VOC emissions by
 wheat (Triticum aestivum) grown in soil inoculum from wheat-fallow or
 wheat-cover crop rotations that was subjected to larval feeding by
 sawflies (Cephus cinctus). Under herbivory, plants grown in cover crop
 inoculum emitted greater total VOCs, including higher concentrations of
 2-pentadecanone, a known insect repellent, and nonanal, a compound
 important in the recruitment of natural enemies of pests. Plants grown in
 fallow inoculum showed no differences in VOC emissions whether under
 herbivory or not. Soil inoculum did not influence VOC emissions of plants
 in the absence of larval feeding. These results suggest that agricultural
 practices influence crop VOC emissions through microbe-mediated soil
 effects. Additionally, crops grown in wheat-fallow rotations may be less
 successful recruiting natural enemies of pests through herbivore-induced
 VOC signaling.
description: The file 'microbesvolatiles.xslx' contains the raw data
 used in our publication 'Soil microbes alter herbivore-induced
 volatile emissions in response to cereal cropping systems'. Please
 see the 'metadata' tabs within the excel file for more detail
 about the data file.
DOI: 10.5061/dryad.jsxksn062
title: Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura

description: While recombination is widely recognized to be a key modulator of numerous
 evolutionary phenomena, we have a poor understanding of how recombination
 rate itself varies and evolves within a species. Here, we performed a
 comprehensive study of recombination rate (rate of meiotic crossing over)
 in two natural populations of Drosophila pseudoobscura from Utah and
 Arizona, USA. We used an amplicon sequencing approach to obtain
 high-quality genotypes in approximately 8000 individual backcrossed
 offspring (17 mapping populations with roughly 530 individuals each), for
 which we then quantified crossovers. Interestingly, variation in
 recombination rate within and between populations largely manifested as
 differences in genome-wide recombination rate rather than remodeling of
 the local recombination landscape. Comparing populations, we discovered
 individuals from the Utah population displayed on average 8% higher
 crossover rates than the Arizona population, a statistically significant
 difference. Using a QST-FST analysis, we found that this difference in
 crossover rate was dramatically higher than expected under neutrality,
 indicating that this difference may have been driven by natural selection.
 Finally, using a combination of short and long read whole-genome
 sequencing, we found no significant association between crossover rate and
 structural variation at the 200-400kb scale. Our results demonstrate that
 (1) there is abundant variation in genome-wide crossover rate in natural
 populations, (2) at the 200-400kb scale, recombination rate appears to
 vary largely genome wide, rather than in specific intervals and (3)
 interpopulation differences in recombination rate may be the result of
 local adaptation.
description: - Primers were designed as described in Samuk et al.
 2020 - We followed the GT-seq library prep protocol in
 Campbell et al. (2017) https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12357 - We sequenced the libraries in two NextSeq 500 lanes at the Duke Genomics Core - We demultiplexed the libraries using fastq-multx, as shown here https://github.com/ksamuk/samuk_et_al_curr_biol_2020/blob/master/analysis_GATK/scripts/01_demultiplex_one_lane.sh
description: - Data set contains paired-end amplicon reads for ~9800
 individuals from 19 separate mapping populations of Drosophila
 pseudoobscura. - Files are named
 like r1.AFC_14_15_A01.fq: r1 = Read 1 (paired
 end)<br> AFC = The source population, AFC = American Fork Canyon, UT
 or MC = Madera Canyon, AZ.<br> 14 = The inbred line ID (this is the
 identifier for the mapping population).<br> 15 = A 96 well plate
 identifier (individuals were collected and prepped in plates)<br>
 A01 = A well indentifier, which also serves as an individual ID.<br>
DOI: 10.5068/d1zm2q
title: Data from: The subcortical basis of outcome and cognitive impairment in TBI: a longitudinal cohort study

description: Objective: To understand how, biologically, the acute event of traumatic
 brain injury gives rise to a long-term disease, we address the
 relationship between evolving cortical and subcortical brain damage and
 measures of functional outcome and cognitive functioning at six months
 post-injury. Methods: Longitudinal analysis of clinical and MRI data
 collected, in a tertiary neurointensive care setting, in a continuous
 sample of 157 patients surviving moderate to severe traumatic brain injury
 between 2000 and 2018. For each patient we collected T1- and T2-weighted
 MRI data, acutely and at a six-months follow-up, as well as acute measures
 of injury severity (Glasgow Coma Scale) and follow-up measures of
 functional impairment (Glasgow Outcome Scale extended), and, in a subset
 of patients, neuropsychological measures of attention, executive
 functions, and episodic memory. Results: In the final cohort of 113
 subcortical and 92 cortical datasets that survived (blind) quality
 control, extensive atrophy was observed over the first six months
 post-injury across the brain. Nonetheless, only atrophy within subcortical
 regions, particularly in left thalamus, were associated with functional
 outcome and neuropsychological measures of attention, executive functions,
 and episodic memory. Furthermore, when brought together in an analytical
 model, longitudinal brain measurements could distinguish good versus bad
 outcome with 90% accuracy, whereas acute brain and clinical measurements
 alone could only achieve 20% accuracy. Conclusion. Despite great injury
 heterogeneity, secondary thalamic pathology is a measurable minimum common
 denominator mechanism directly relating biology to clinical measures of
 outcome and cognitive functioning, potentially linking the acute “event”
 and the longer-term “disease” of TBI.
description: These materials are a supplement to the text in the manuscript
 "The subcortical basis of outcome and cognitive impairment in TBI: a
 longitudinal cohort study" by Evan S. Lutkenhoff, PhD, Matthew J.
 Wright, PhD, Vikesh Shrestha, BS, Courtney Real, MSN, David L. McArthur,
 PhD, MPH, Manuel Buitrago-Blanco, MD, PhD, Paul M. Vespa, MD, Martin M.
 Monti, PhD. This supplement includes the
 following content: <b>Table S1</b>.
 Shape analysis results (Time). <b>Table S2</b>.
 Shape analysis results (Outcome). <b>Table S3</b>.
 Shape analysis results (Cognitive impairment analysis: Attention).
   <b>Table
 S4</b>. Shape analysis results (Cognitive impairment analysis:
 Executive Functions).   <b>Table S5</b>.
 Shape analysis results (Cognitive impairment analysis: Episodic
 Memory). <b>Table S6</b>.
 Modeling analysis results (Outcome). <b>Table S7</b>.
 Modeling analysis results (Cognitive impairment).
DOI: 10.5061/dryad.qv9s4mwbb
title: Memory reactivation in rat medial prefrontal cortex occurs in a subtype of cortical UP state during slow-wave sleep

description: Interaction between hippocampal sharp-wave ripples (SWRs) and UP states,
 possibly by coordinated reactivation of memory traces, is conjectured to
 play an important role in memory consolidation. Recently, it was reported
 that SWRs were differentiated into multiple subtypes. However, whether
 cortical UP states can also be classified into subtypes is not known.
 Here, we analysed neural ensemble activity from the medial prefrontal
 cortex from rats trained to run a spatial sequence-memory task.
 Application of the hidden Markov model (HMM) with three states to epochs
 of UP–DOWN oscillations identified DOWN states and two subtypes of UP
 state (UP-1 and UP-2). The two UP subtypes were distinguished by
 differences in duration, with UP-1 having a longer duration than UP-2, as
 well as differences in the speed of population vector (PV) decorrelation,
 with UP-1 decorrelating more slowly than UP-2. Reactivation of recent
 memory sequences predominantly occurred in UP-2. Short-duration
 reactivating UP states were dominated by UP-2 whereas long-duration ones
 exhibit transitions from UP-1 to UP-2. Thus, recent memory reactivation,
 if it occurred within long-duration UP states, typically was preceded by a
 period of slow PV evolution not related to recent experience, and which we
 speculate may be related to previously encoded information. If that is the
 case, then the transition from UP-1 to UP-2 subtypes may help gradual
 integration of recent experience with pre-existing cortical memories by
 interleaving the two in the same UP state. This article is part of the
 Theo Murphy meeting issue ‘Memory reactivation: replaying events past,
 present and future'.
DOI: 10.5061/dryad.1jwstqjrg
title: Individual variation in parental tradeoffs between the number and size of offspring at the pre- and post-natal stages

description: Life-history theory predicts that parents refer to the resources they hold
 to determine their breeding strategy. In multi-brooded species, it is
 hypothesized that single-brooded parents produce larger clutches and raise
 offspring with a brood survival strategy, whilst multi-brooded parents
 only do this under good breeding conditions. Under poor conditions, they
 produce smaller clutches and raise offspring with a brood reduction
 strategy. We tested this hypothesis in the Brown-cheeked Laughing Thrush
 Trochalopteron henrici, which can breed twice a year on the Tibetan
 Plateau, by investigating the life-history traits and provisioning
 behaviours of single- and double-brooded parents. Single-brooded parents
 laid larger clutches of smaller eggs and produced more and larger
 fledglings than double-brooded parents in their first brood.
 Double-brooded parents produced smaller clutches of larger eggs but
 fledged larger nestlings in their first brood than in their second brood.
 As single-brooded parents only need to raise one brood a year, then
 producing and raising as many offspring as possible (i.e., the brood
 survival strategy in a large brood) can maximize their reproductive
 success. For double-brooded parents, producing and raising fewer offspring
 in the first brood (i.e., the brood survival strategy in a small brood)
 can ensure their nesting success during a short breeding cycle.
 Additionally, producing more offspring but raising larger nestlings in the
 second brood (i.e., the brood reduction strategy in a large brood) can
 select for offspring of higher quality within the brood. Our findings
 indicate that different tradeoffs between single- and double-brooded
 parents in egg-laying and nestling-raising may be an adaptation to the
 seasonal variation in environmental conditions.
description: This dataset had been collected in the filed. It has not been
 processed.
DOI: 10.5061/dryad.12jm63xts
title: Optical traits perform equally well as directly-measured functional traits in explaining the impact of an invasive plant on litter decomposition

description: 1. Functional traits can help elucidate and predict the impact of invasive
 plant species on ecosystem functioning. Yet, this approach requires
 comprehensive and labor-intensive trait collection campaigns, covering
 intraspecific trait variation of both the invader and native species in
 the invaded community. One potential way to overcome these logistic
 constraints is using hyperspectral remote sensing technology to
 efficiently quantify functional trait values. Although such spectrally
 derived or ‘optical’ traits are known to closely link to directly-measured
 functional traits, little research has explored how well these optical
 traits perform in assessing invader-induced ecosystem impact. 2. Here, we
 explored the trait-mediated impact of the invasive Rosa rugosa on litter
 decomposition and evaluated whether optical traits perform equally well as
 directly-measured traits in predicting litter decomposition variation. We
 collected data on species-specific functional traits, leaf hyperspectral
 reflectance and standardized ‘tea bag index’ litter decomposition across
 25 invaded and 25 uninvaded coastal grassland plots. The selected traits
 were all potentially related to litter decomposition and covered the leaf
 economics spectrum, additional leaf structural components and competitive
 ability. Optical traits were quantified through a combination of a
 physical radiative transfer model inversion and vegetation indices
 calculations. 3. Invasion significantly increased the stabilization
 factor, i.e. the amount of resulting recalcitrant litter. Invader impact
 on litter decomposition could be entirely explained by changes it induced
 in the functional traits of the native community, rather than by the
 invader’s traits itself. More specifically, the invader pushed the invaded
 community towards traits associated with high litter quality. Optical
 traits performed equally well as directly-measured traits in explaining
 the invasion impact on the stabilization factor (R2= 41.9% vs. 38.5%).
 Furthermore, the interpretation of the results based on optical traits
 resulted in a similar functional understanding of the invader impact. 4.
 Synthesis: Our results indicate the potential of hyperspectral data to
 explain changes in ecosystem functioning. The combination of radiative
 transfer models and vegetation indices allowed to extract all relevant
 trait information from the hyperspectral data. This framework thus
 presents a practical short-cut to assess relevant leaf traits, requiring
 only a limited amount of field trait measurements.
description: See the linked Helsen et al. (2020) Journal of Ecology paper
description: Rosa_plot_level_dataset.xls: 'dataset' tab contains all
 plot level information: plot code, invasion status, patch ID and all
 litter, species composition, functional trait and optical trait
 information. Rosa_plot_level_dataset.xls:
 'Metadata' tab contains units and description of all variables
 presented in the 'dataset' tab.
DOI: 10.5061/dryad.nk98sf7qm
title: Presence locations (direct and indirect) of blue sheep and livestock in Johar Valley, Uttarakhand, India from years 2015-2017

description: In-depth knowledge of distribution and their factors are important for
 species conservation and management. Many forms of such data have led to
 development of new analytical techniques for better interpretation. For
 mountainous terrains with certain limitations, species data is obtained in
 presence-only form. Point process model is one of the recent approaches
 for modelling such data, taking care of pseudo-absences and spatial
 independence. For conservation of regions with limited resources and
 species with similar ecological requirements, it is important to properly
 assess competition extent between wild and domestic species. We attempted
 to use point process framework to estimate resource selection function of
 blue sheep (Pseudois nayaur) in pastoralism influenced areas of a western
 Himalayan landscape. Our study is a first attempt to use this framework to
 estimate resource selection on a dataset not collected using
 radio-telemetry. Spatial locations of presence points of blue sheep and
 livestock and a background sample of random points along with six
 topographic covariates were used for modelling resource selection
 probability via intensity function. Blue sheep showed its predicted
 presence in areas with open vegetation coinciding with alpine meadows,
 influenced by southern aspect keeping a threshold distance of 600m-1000m
 from cliffs (escape terrain). Livestock, also showed presence probability
 in open vegetation but at lower altitudes mainly on valley floors. Our
 results suggest that though blue sheep continued to use the same habitat
 type after livestock arrival, they selected different resources based on
 topographic factors. Livestock were in areas convenient for pastoralists
 for establishing their campsites and feasibility of grazing along with
 presence of nutritious grasses. Thus, we assume that probable shift of
 habitat for blue sheep from optimal areas occurs due to livestock
 presence, which might disturb their nutritional balance. Our study
 provides helpful insights for management of rangelands, which when tied
 with dietary patterns will give wholesome idea for proper conservation
 measures in future.
DOI: 10.5061/dryad.qrfj6q5c1
title: Data from: Evaluating predictive performance of statistical models explaining wild bee abundance in a mass-flowering crop

description: Wild bee populations are threatened by current agricultural practices in
 many parts of the world, which may put pollination services and crop
 yields at risk. Loss of pollination services can potentially be predicted
 by models that link bee abundances with landscape-scale land-use, but
 there is little knowledge on the degree to which these statistical models
 are transferable across time and space. This study assesses the
 transferability of models for wild bee abundance in a mass-flowering crop
 across space (from one region to another) and across time (from one year
 to another). The models used existing data on bumblebee and solitary bee
 abundance in winter oilseed rape fields, together with high-resolution
 land-use crop-cover and semi-natural habitats data, from studies conducted
 in five different regions located in four countries (Sweden, Germany,
 Netherlands, and the UK), in three different years (2011, 2012, 2013). We
 developed a hierarchical model combining all studies and evaluated the
 transferability using cross-validation. We found that both the
 landscape-scale cover of mass-flowering crops and permanent semi-natural
 habitats, including grasslands and forests, are important drivers of wild
 bee abundance in all regions. However, while the negative effect of
 increasing mass-flowering crops on the density of the pollinators is
 consistent between studies, the direction of the effect of semi-natural
 habitat is variable between studies. The transferability of these
 statistical models is limited, especially across regions, but also across
 time. Our study demonstrates the limits of using statistical models in
 conjunction with widely available land-use crop-cover classes for
 extrapolating pollinator density across years and regions, likely in part
 because input variables such as cover of semi-natural habitats poorly
 capture variability in pollinator resources between regions and years.