cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.brv15dv6c
title: High-quality genome assembly of Chrysaora quinquecirrha provides insights into the adaptive evolution of jellyfish

description: Jellyfish, such as Chrysaora quinquecirrha, hold an important evolutionary
 position and have great ecological value. However, limited genomic
 resources are currently available for studying their basic genetic and
 development processes. Here, we de novo assembled the first high-quality
 reference genome of C. quinquecirrha, and successfully annotated 18,644
 protein-coding genes. Codon usage analysis identified the frequent use of
 low-GC-content codons during protein-coding gene translation. Analysis of
 the relative evolution rate indicated that jellyfish had a faster
 evolution rate than sea anemones but slower rate than the species in
 Hydrozoa. Phylogenetic analysis with two other species of jellyfish
 indicated that Aurelia aurita and Nemopilemanomurai have a closer
 relationship with each other than with C. quinquecirrha, with divergence
 from their common ancestor occurring approximately 476.5 million years
 ago. Furthermore, comparative genomics analysis identified that the
 biological muscle contraction pathways were specifically enriched in all
 three jellyfish genomes, suggesting these genes may have great
 contributions in the muscle contraction movement process of jellyfishes.
 Our study not only showed the genomic characteristics and molecular
 adaptive evolution of C. quinquecirrha, but also provides valuable genomic
 resources for further study on complex developmental processes and
 environmental adaptations.
DOI: 10.5061/dryad.c866t1g3t
title: Combining GWAS and FST-based approaches to identify targets of Borrelia-mediated selection in natural rodent hosts

description: Recent advances in high-throughput sequencing technologies provide
 opportunities to gain novel insights into the genetic basis of phenotypic
 trait variation. Yet to date, progress in our understanding of
 genotype-phenotype associations in non-model organisms in general and
 natural vertebrate populations in particular has been hampered by small
 sample sizes typically available for wildlife populations and a resulting
 lack of statistical power, as well as a limited ability to control for
 false positive signals. Here we propose to combine a genome-wide
 association (GWAS) and FST-based approach with population-level
 replication to partly overcome these limitations. We present a case study
 in which we used this approach in combination with
 Genotyping-by-Sequencing (GBS) SNP data to identify genomic regions
 associated with Borrelia afzelii resistance or susceptibility in the
 natural rodent host of this Lyme disease-causing spirochete, the bank vole
 (Myodes glareolus). Using this combined approach we identified four
 consensus SNPs located in exonic regions of the genes Slc26a4, Tns3, Wscd1
 and Espnl, which were significantly associated with the voles’ Borrelia
 infectious status within and across populations. Functional links between
 host responses to bacterial infections and most of these genes have
 previously been demonstrated in other rodent systems, making them
 promising new candidates for the study of evolutionary host responses to
 Borrelia emergence. Our approach is applicable to other systems and may
 facilitate the identification of genetic variants underlying disease
 resistance or susceptibility, as well as other ecologically relevant
 traits, in wildlife populations.
DOI: 10.15468/dl.fzk4x9
title: Occurrence Download

description: A dataset containing 920 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudophycis bachus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 920 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002247-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s1rn8pk4k
title: Extreme weather affects colonization-extinction dynamics and the persistence of a threatened butterfly

description: 1. Extreme weather events can be expected to increase in frequency in the
 future. Our knowledge on how this may affect species persistence is,
 however, very limited. For reliable projections of future persistence we
 need to understand how extreme weather affects species’ population
 dynamics. 2. We analysed the effect of extreme droughts on the host plant
 (Succisa pratensis), colonization-extinction dynamics, and future
 persistence of the threatened marsh fritillary (Euphydryas aurinia).
 Specifically, we studied a metapopulation inhabiting a network of 256
 patches on Gotland (Sweden), where the summer of 2018 was the driest ever
 recorded. We analysed how the frequency and leaf size of host plants
 changed between 2017 and 2019, based on 6833 records in 0.5 m2 sample
 plots. Using turnover data on the butterfly from 2018 to 2019 we modelled
 local extinction and colonization probabilities. Moreover, we projected
 future population dynamics with an increasing frequency of extreme years
 under three different management strategies that regulate the grazing
 regime. 3. Our results show a substantial decrease in both frequency (46%)
 and size (20%) of host plants due to the drought, which taken together may
 constitute a 57% loss of food resources. The butterfly occupancy decreased
 by over 30% between 2018 and 2019 (from 0.36 to 0.27). The extinction
 probability increased with increasing ‘effective area’ of the patch
 (taking quality reduction due to grazing into account), and the
 colonization probability increased with increasing connectivity and ground
 moisture. 4. Projections of future dynamics showed an increasing risk of
 metapopulation extinction with increasing frequency of years with extreme
 droughts. The risk, however, clearly differed between management
 strategies. Less grazing in years with droughts decreased the extinction
 risk considerably. 5. Synthesis and applications: Extreme weather events
 can have profound negative impacts on butterflies and their host plants.
 For the marsh fritillary, an increased frequency of extreme droughts can
 lead to extinction of the entire metapopulation, even in a large and
 seemingly viable metapopulation. Increased grazing, due to fodder
 deficiency in dry years, may lead to cascading negative effects, while
 active management that reduce grazing in years with droughts can almost
 completely mitigate these effects.
DOI: 10.5061/dryad.70rxwdbtg
title: Data from: Plant community composition steers grassland vegetation via soil legacy effects

description: Soil legacy effects are commonly highlighted as drivers of plant community
 dynamics and species co-existence. However, experimental evidence for soil
 legacy effects of conditioning plant communities on responding plant
 communities under natural conditions is lacking. We conditioned 192
 grassland plots using six different plant communities with different
 ratios of grasses and forbs and for different durations. Soil microbial
 legacies were evident for soil fungi, but not for soil bacteria, while
 soil abiotic parameters did not significantly change in response to
 conditioning. The soil legacies affected the composition of the succeeding
 vegetation. Plant communities with different ratios of grasses and forbs
 left soil legacies that negatively affected succeeding plants of the same
 functional type. We conclude that fungal-mediated soil legacy effects play
 a significant role in vegetation assembly of natural plant communities.
description: Vegetation recordings were assessed by visual estimation of each
 plant species present. Nine soil samples were taken and
 pooled per subplot and these were homogenized as a representitive subplot
 sample. A subsample was taken for bacterial (16S) and fungal (ITS2)
 sequencing.  For further extensive methodology, see
 Heinen et al. (2020) Ecology Letters.
description: Usage notes are included in the data file under the
 "Notes" tab.
DOI: 10.5061/dryad.18931zcst
title: Unravelling the habitat preferences of two closely related bumble bee species in Eastern Europe

description: Co-occurrence of closely related species is often explained through
 resource partitioning, where key morphological or life-history traits
 evolve under strong divergent selection. In bumble bees (genus Bombus),
 differences in tongue lengths, nest sites, and several life-history traits
 are the principal factors in resource partitioning. However, the
 buff-tailed and white-tailed bumble bee (Bombus terrestris and B. lucorum
 respectively) are very similar in morphology and life-history, but their
 ranges nevertheless partly overlap, raising the question how they are
 ecologically divergent. What little is known about the environmental
 factors determining their distributions stems from studies in Central and
 Western Europe, but even less information is available about their
 distributions in Eastern Europe, where different subspecies occur. Here,
 we aimed to disentangle the broad habitat requirements and associated
 distributions of these species in Romania and Bulgaria. First, we
 genetically identified sampled individuals from many sites across the
 study area. We then not only computed species distributions based on
 presence-only data, but also expanded on these models using relative
 abundance data. We found that B. terrestris is a more generalist species
 than previously thought, but that B. lucorum is restricted to forested
 areas with colder and wetter climates, which in our study area are
 primarily found at higher elevations. Both vegetation parameters such as
 annual mean Leaf Area Index and canopy height, as well as climatic
 conditions were important in explaining their distributions. Although our
 models based on presence-only data suggest a large overlap in their
 respective distributions, results on their relative abundance suggest that
 the two species replace one another across an environmental gradient
 correlated to elevation. The inclusion of abundance enhances our
 understanding of the distribution of these species, supporting the
 emerging recognition of the importance of abundance data in species
 distribution modeling.
DOI: 10.5061/dryad.dbrv15dxp
title: Predictability of food supply modulates nocturnal hypothermia in a small passerine

description: The combination of short days and long cold nights in winter, in temperate
 regions, presents a major challenge for small diurnal birds. Small birds
 regularly employ heterothermy and enter rest-phase hypothermia during
 winter nights to conserve energy. However, we know little about how
 environmental conditions, such as food availability, shape these
 strategies. Using an experimental set-up, we manipulated food availability
 in winter to free-living great tits Parus major. A “predictable” and
 constant food supply was provided to birds in one area of a forest, while
 birds in another area did not have access to a reliable supplementary food
 source. We found that predictability of food affected the extent of
 nocturnal hypothermia, but the response differed between sexes. Whereas
 male nocturnal body temperature was similar regardless of food
 availability, females exposed to a naturally “unpredictable” food supply
 entered deeper hypothermia at night, compared with females that had access
 to predictable food and compared with males in both treatment groups. We
 suggest that this response likely is a consequence of dominance, and the
 subdominant females cannot maintain sufficient energy intake, resulting in
 a higher demand for energy conservation at night.
description: Body temperature measurements of wild great tits in relation to
 predictability of food supply.
DOI: 10.15468/dl.ehu8au
title: Occurrence Download

description: A dataset containing 118489 records in GBIF matching the query:
SELECT
 '426' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -125.88796183592417
 AND decimalLongitude &lt;= -113.8874202948881
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 118489 records were derived from 350 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002230-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3bk3j9kfw
title: Clinical outcomes in multifocal motor neuropathy: a combined cross-sectional and follow-up study

description: Objective To assess the clinical course of multifocal motor neuropathy
 (MMN) in a large cohort of patients and to identify predictive factors of
 a progressive disease course. Methods Between May 2015 and February 2016,
 we collected clinical data from 100 patients with MMN of whom 60 had
 participated in a nationwide cross-sectional cohort study in 2007. We
 documented clinical characteristics using standardized questionnaires and
 performed a standardized neurological examination. We used multiple linear
 regression analysis to identify factors that correlated with worse
 outcome. Results We found that age of diagnosis (45.2 vs. 48.6 years,
 p&lt;0.02) significantly increased between 2007 and 2015-2016, whereas
 diagnostic delay decreased with 15 months. Seven out of ten outcome
 measures deteriorated over time (all p&lt;0.01). Patients who had a
 lower MRC sum score and absence of one or more reflexes at the baseline
 visit showed a greater functional loss at follow up (p=0.007 and p=0.016).
 Conclusions Our study shows that MMN is a progressive disease. Although
 87% of patients received maintenance treatment, muscle strength, reflexes,
 vibration sense, and the Self-Evaluation Scale significantly deteriorated
 over time. Lower MRC sum score and absence of reflexes predicted a more
 progressive disease course. Classification of evidence This study provides
 Class II evidence that lower MRC sum score and the absence of reflexes
 predict a more progressive disease course in patients with MMN.
DOI: 10.5061/dryad.bg79cnp7s
title: Data from: The costs and benefits of paternal care in fish: a meta-analysis

description: Male-only parental care, while rare in most animals, is a widespread
 strategy within teleost fish. The costs and benefits to males of acting as
 sole carer are highly variable between fish species making it challenging
 to determine the selective pressures driving the evolution of male-only
 care to such a high prevalence. We conducted a phylogenetic meta-analysis
 to examine the costs and benefits of paternal care across fish species. We
 found no evidence that providing care negatively affects male condition.
 In contrast to other taxa, we also found limited evidence that male care
 has evolved as a strategy to improve offspring survival. Instead, we found
 that males already caring for a brood are preferred by females and that
 this preference is strongest in those species in which males work harder
 to care for larger broods. Thus, in fish, investment in offspring care
 does not constrain a male’s mating success but rather augments it,
 suggesting that the relatively high prevalence of male-only care in fish
 may be in part explained by sexual selection through female preference for
 caring males. 
description: Details of all files given in README.txt file
DOI: 10.5061/dryad.bk3j9kd78
title: Brain size, gut size and cognitive abilities: the energy trade-offs tested in artificial selection experiment

description: The enlarged brains of homeotherms bring behavioural advantages, but also
 incur high energy expenditures. The ‘Expensive Brain’ (EB) hypothesis
 posits that the energetic costs of the enlarged brain and the resulting
 increased cognitive abilities (CA) were met either by increased energy
 turnover or reduced allocation to other expensive organs, such as the gut.
 We tested the EB hypothesis by analyzing correlated responses to selection
 in an experimental evolution model system, which comprises line types of
 laboratory mice selected for high or low basal (BMR), or high maximum
 (VO2max) metabolic rates. The traits are implicated in the evolution of
 homeothermy, having been pre-requisites for the encephalisation and
 exceptional CA of mammals, including humans. High-BMR mice had bigger
 guts, but not brains, than mice of other line types. Yet, they were
 superior to the other line types in the cognitive tasks carried out in
 both reward and avoidance learning contexts. Furthermore, the high-BMR
 mice had higher neuronal plasticity (indexed as the long-term
 potentiation, LTP) than their counterparts. Our data indicate that the
 evolutionary increase of CA in mammals was initially associated with
 increased BMR and brain plasticity. It was also fueled by an enlarged gut,
 which was not traded off for brain size.
description: All information on data collection and processing is provided in
 the manuscript and Supplementary Materials.
description: Goncerzewicz_et_al_data.xls File contains raw
 data on individual measurements of Basal Metabolic Rate (BMR), body and
 internal organ masses (including brain), assessments of locomotor activity
 and reward-motivated discrimination learning along with data long-term
 potentiation (LTP), a
 classical model for investigation of activity-dependent synaptic
 plasticity. Detailed description of all measured variables is provided in
 Spreadsheet legend.
DOI: 10.5061/dryad.v41ns1rs5
title: Data from: Social and emotional contexts predict the development of gaze following in early infancy

description: The development of gaze following begins in early infancy and its
 developmental foundation has been under heavy debate. Using a longitudinal
 design (N = 118), we demonstrate that attachment quality predicts
 individual differences in the onset of gaze following, at 6 months of age,
 and that maternal postpartum depression predicts later gaze following, at
 10 months. In addition, we report longitudinal stability in gaze following
 from 6 to 10 months. A full path model (using attachment, maternal
 depression, and gaze following at 6) accounted for 21 % of variance in
 gaze following at 10 months. These results suggest an experience-dependent
 development of gaze following, driven by the infant’s own motivation to
 interact and engage with others (the social-first perspective).
description: Gaze data was exported from Tobii Studio and processed in MATLAB
 version R2017b (9.3.0. 713579) using TimeStudio (version 3.18). See the
 time series analyses file BASIC_GF.study and visit timestudioproject.com
 for user instructions.  Maternal postpartum depression
 was assessed using the Edinburgh Postnatal Depression Scale (EPDS) at 6
 weeks, 6 months, and 12 months after child delivery.
 The SSP was used to assess infant-mother attachment quality when
 the child was 12 months old. Two certified coders rated attachment
 according to the ABCD classification, providing a B (secure) vs. ACD
 (non-secure) score. For more information about the social context
 measures, including data reduction, see the Supplementary.
description: <strong>This is the R code used for the path
 analysis:</strong> library(lavaan)
 library(influence.SEM)  
 GF_data &lt;- read.csv2('BASIC_GF.csv')
   Model &lt;- '
 GF_10 ~ GF_6 + Dep12mpp + Dep6mpp + Dep6vpp + BvsACD
 GF_6 ~ Dep6mpp + Dep6vpp  + BvsACD Dep12mpp ~
 Dep6mpp + BvsACD Dep6mpp ~ Dep6vpp + BvsACD
 Dep6vpp ~ BvsACD '
 gCD.mod&lt;-
 genCookDist(Model,data=GF_data,std.lv=TRUE)
 plot(gCD.mod,pch=19,xlab="observations",ylab="Cook
 distance") GF_data.gCDExc &lt;-
 GF_data[-which(gCD.mod&gt;1),] Model.fit &lt;-
 sem(Model, data = GF_data.gCDExc, estimator = 'ML',
 missing='fiml', std.ov = TRUE)
 summary(Model.fit, fit.measures = TRUE,standardize = TRUE,
 rsquare = TRUE)
DOI: 10.5061/dryad.mkkwh70w4
title: Floral density and co-occurring congeners alter patterns of selection in annual plant communities

description: While the evolution and diversification of flowers is often attributed to
 pollinator-mediated selection, interactions between co-occurring plant
 species can alter patterns of selection mediated by pollinators and other
 agents. The extent to which both floral density and congeneric species
 richness affect patterns of net and pollinator-mediated selection on
 multiple co-occurring species in a community is unknown and is likely to
 depend on whether co-occurring plants experience competition or
 facilitation for reproduction. We conducted an observational study of
 selection on four species of Clarkia (Onagraceae) and tested for
 pollinator-mediated selection on two Clarkia species in communities
 differing in congeneric species richness and local floral density. When
 selection varied with community context, selection was generally stronger
 in communities with fewer species, where local conspecific floral density
 was higher, and where local heterospecific floral density was lower. These
 patterns suggest that intraspecific competition at high densities and
 interspecific competition at low densities may affect the evolution of
 floral traits. However, selection on floral traits was not
 pollinator-mediated in C. cylindrica or C. xantiana, despite variation in
 pollinator visitation and the extent of pollen limitation across
 communities for C. cylindrica. As such, interactions between co-occurring
 species may alter patterns of selection mediated by abiotic agents of
 selection.
description: All procedures for data collection and processing are listed in
 the manuscript. The units for each variable are in the datadescriptors.csv
 file.
description: The uploaded files contain raw values and the standardized values
 that were used in the analyses in the paper. Missing values are marked
 with NA and occurred when plants were damaged in the field or when certain
 measurements were not recorded due to user error. There is a
 datadescriptors.csv file that contains descriptions of each column in all
 three data files.