cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jq0t8rc4
title: Data from: Historical and ecological controls on phylogenetic diversity in Californian plant communities

description: We addressed the classic question of whether community diversity is
 determined from the bottom up by the breadth and partitioning of niche
 space or from the top down by historical and evolutionary forces.
 Specifically, we contrasted local and regional explanations for the
 diversity of Californian plant communities using phylogenetic and
 functional analyses. Our communities were sets of four field plots that
 sampled alpha (within-plot) and beta (among-plot) sources of variation in
 diversity. We sampled 93 such communities nested within 78 larger regions
 for which regional species pools could be independently estimated,
 spanning the California Floristic Province. We measured phylogenetic and
 functional diversity within plots and between plots on neighboring soils
 and slopes. We also measured the phylogenetic diversity of regional
 species pools and analyzed them in terms of biogeographic groups. We found
 no evidence linking the phylogenetic diversity of communities to
 within-plot functional diversity or among-plot beta diversity. Instead, we
 found that the phylogenetic diversity of communities depends on that of
 regional species pools. In turn, phylogenetically diverse pools were those
 with high proportions of species of northern biogeographic affinity, which
 have relatively mesic distributions and traits. This supports what we call
 the climatic refuge hypothesis rather than the biogeographic crossroads
 hypothesis.
description: dryad
DOI: 10.5061/dryad.cj432
title: Data from: QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici

description: Different thermal environments impose strong, differential selection on
 populations, leading to local adaptation, but the genetic basis of thermal
 adaptation is poorly understood. We used quantitative trait locus (QTL)
 mapping in the fungal wheat pathogen Zymoseptoria tritici to study the
 genetic architecture of thermal adaptation and identify candidate genes.
 Four wild-type strains originating from the same thermal environment were
 crossed to generate two mapping populations with 263 (cross 1) and 261
 (cross 2) progeny. Restriction site-associated DNA sequencing was used to
 genotype 9745 (cross 1) and 7333 (cross 2) single-nucleotide polymorphism
 markers segregating within the mapping population. Temperature sensitivity
 was assessed using digital image analysis of colonies growing at two
 different temperatures. We identified four QTLs for temperature
 sensitivity, with unique QTLs found in each cross. One QTL had a logarithm
 of odds score &gt;11 and contained only six candidate genes, including
 PBS2, encoding a mitogen-activated protein kinase kinase associated with
 low temperature tolerance in Saccharomyces cerevisiae. This and other QTLs
 showed evidence for pleiotropy among growth rate, melanization and growth
 morphology, suggesting that many traits can be correlated with thermal
 adaptation in fungi. Higher temperatures were highly correlated with a
 shift to filamentous growth among the progeny in both crosses. We show
 that thermal adaptation has a complex genetic architecture, with natural
 populations of Z. tritici harboring significant genetic variation for this
 trait. We conclude that Z. tritici populations have the potential to adapt
 rapidly to climate change and expand into new climatic zones.
description: Phenotypes for QTL
 mappingGrowth rate (mm day-1),
 temperature sensitivity and yeast/hyphae dimorphism phenotypes for the
 quality filtered retained progeny used in the QTL analysis for each of the
 two crosses.Absolute and relative
 phenotypes as well as the yeast_hyphae scores for the retained progeny of
 each cross.docx
DOI: 10.5061/dryad.6j2c875
title: Data from: Diffusion tensor imaging reveals diffuse white matter injuries in locked-in syndrome patients

description: Locked-in syndrome (LIS) is a state of quadriplegia and anarthria with
 preserved consciousness, which is generally triggered by a disruption of
 specific white matter fiber tracts, following a lesion in the ventral part
 of the pons. However, the impact of focal lesions on the whole brain white
 matter microstructure and structural connectivity pathways remains
 unknown. We used diffusion tensor magnetic resonance imaging (DT-MRI) and
 tract-based statistics to characterise the whole white matter tracts in
 seven consecutive LIS patients, with ventral pontine injuries but no
 significant supratentorial lesions detected with morphological MRI. The
 imaging was performed in the acute phase of the disease (26 ± 13 days
 after the accident). DT-MRI-derived metrics were used to quantitatively
 assess global white matter alterations. All diffusion coefficient Z-scores
 were decreased for almost all fiber tracts in all LIS patients, with
 diffuse white matter alterations in both infratentorial and supratentorial
 areas. A mixture model of two multidimensional Gaussian distributions was
 fitted to cluster the white matter fiber tracts studied in two groups: the
 least (group 1) and most injured white matter fiber tracts (group 2). The
 greatest injuries were revealed along pathways crossing the lesion
 responsible for the LIS: left and right medial lemniscus (98.4% and 97.9%
 probability of belonging to group 2, respectively), left and right
 superior cerebellar peduncles (69.3% and 45.7% probability) and left and
 right corticospinal tract (20.6% and 46.5% probability). This approach
 demonstrated globally compromised white matter tracts in the acute phase
 of LIS, potentially underlying cognitive deficits.
description: FA Z-scores
 tableFA Z-scores table
 represents the set of values of FA Z-scores for the seven LIS
 patients.MD Z-scores
 tableMD Z-scores table
 represents the set of values of MD Z-scores for the seven LIS
 patients.AD Z-scores
 tableAD Z-scores table
 represents the set of values of AD Z-scores for the seven LIS
 patients.RD Z-scores
 tableRD Z-scores table
 represents the set of values of RD Z-scores for the seven LIS
 patients.
DOI: 10.5061/dryad.8265
title: Data from: Population divergence in chemical signals and the potential for premating isolation between islet- and mainland populations of the Skyros wall lizard, (Podarcis gaigeae)

description: When sexually selected traits diverge due to different local selective
 environments premating isolation might arise as a correlated response.
 However, sexually selected traits might also diverge by stochastic forces.
 Here, we show that odour-based mate preferences and scent composition have
 diverged between islet- and mainland populations of Skyros wall lizard,
 Podarcis gaigeae. We quantified the degree of scent-mediated premating
 isolation between populations. Islet lizards preferred scent from islet
 lizards, whereas the mainland populations were less discriminatory. The
 pheromone compositions differed more between islets than between islet-
 and mainland populations, and did not differ significantly between
 mainland populations. There was a tendency for population divergence in
 pheromones to be positively correlated with neutral genetic divergence.
 This might indicate a role for genetic drift in evolutionary change in
 these signals and partial decoupling between signals and preferences. Our
 results suggest that chemical signals and associated mate preferences can
 diverge through stochastic and selective forces and influence premating
 isolation.
description: Chemical interest trial
 data Runemark et al.Pheromone composition
 data Runemark et al.
DOI: 10.5061/dryad.b91d1
title: Data from: Repeatability of locomotor performance and of morphology - locomotor performance relationships

description: There is good evidence that natural selection drives the evolution of
 locomotor performance, but the processes that generate among individual
 variation in locomotion, the substrate upon which selection acts, are
 relatively poorly understood. We measured prolonged swimming performance,
 Ucrit, and morphology in a large cohort (n=461) of wildtype zebrafish,
 Danio rerio, at ∼6 months and again at ∼9 months. Using mixed model
 analyses to estimate repeatability as the intraclass correlation
 coefficient, we determined that Ucrit was significantly repeatable (r =
 0.55; 95% CI: 0.45 -0.64). Performance differences between the sexes
 (males 12% faster than females) and changes with age (decreasing 0.07% per
 day) both contributed to variation in Ucrit and, therefore, the
 repeatability estimate. Accounting for mean differences between sexes
 within the model decreased the estimate of Ucrit repeatability to 21%
 below the naïve estimate, while fitting age in the models increased the
 estimate to 14% above the naïve estimate. Greater consideration of factors
 such as age and sex is therefore necessary for the interpretation of
 performance repeatability in wild populations. Body shape significantly
 predicted Ucrit in both sexes in both assays, with the morphology –
 performance relationship significantly repeatable at the population level.
 However, morphology was more strongly predicative of performance in older
 fish, suggesting a change in the contribution of morphology relative to
 other factors such as physiology and behaviour. The morphology –
 performance relationship changed with age to a greater extent in males
 than females.
description: Growth_and_Performance_dataDataset associated with regression analysis addressing the question of whether changes in body shape between repeated measures of individuals was statistically associated with changes in Ucrit between repeated measuresmorph_performance_regression_dataData associated with analysis of change in morphology between repeated measures of an individual, and with regression analysis of relationship between morphology and swimming speed (Ucrit) measured at two time points ~3 months apart.Ucrit_repeatabilityData associated with analysis of repeatability of Ucrit swimming performance
DOI: 10.5061/dryad.8fv83
title: Data from: Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas

description: Understanding the distribution of genetic diversity in the light of past
 demographic events linked with climatic shifts will help to forecast
 evolutionary trajectories of ecosystems within the current context of
 climate change. In this study, mitochondrial sequences and microsatellite
 loci were analysed using traditional population genetic approaches
 together with Bayesian dating and the more recent approximate Bayesian
 computation scenario testing. The genetic structure and demographic
 history of a commercial fish, the black scorpionfish, Scorpaena porcus,
 was investigated throughout the Mediterranean and Black Seas. The results
 suggest that the species recently underwent population expansions, in both
 seas, likely concomitant with the warming period following the Last
 Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic
 differentiation was identified between the Black Sea and the Mediterranean
 Sea. However, the genetic diversity was similar for populations of the two
 seas, suggesting a high number of colonizers entered the Black Sea during
 the interglacial period and/or the presence of a refugial population in
 the Black Sea during the glacial period. Finally, within seas, an
 east/west genetic differentiation in the Adriatic seems to prevail,
 whereas the Black Sea does not show any structured spatial genetic pattern
 of its population. Overall, these results suggest that the Black Sea is
 not that isolated from the Mediterranean, and both seas revealed similar
 evolutionary patterns related to climate change and changes in sea level.
description: Scorpaena_porcus_175sequencesalignment of the 175 cytochrome b sequences of Scorpaena porcus used in the analysesScorpaena_porcus_670_genotypesMultilocus genotypes for the 670 specimens of Scorpaena porcus analysed at 11 loci.
DOI: 10.5061/dryad.6620j
title: Data from: Heart rate reveals torpor at high body temperatures in lowland tropical free-tailed bats

description: Reduction in metabolic rate and body temperature is a common strategy for
 small endotherms to save energy. The daily reduction in metabolic rate and
 heterothermy, or torpor, is particularly pronounced in regions with a
 large variation in daily ambient temperature. This applies most strongly
 in temperate bat species (order Chiroptera), but it is less clear how
 tropical bats save energy if ambient temperatures remain high. However,
 many subtropical and tropical species use some daily heterothermy on cool
 days. We recorded the heart rate and the body temperature of free-ranging
 Pallas' mastiff bats (Molossus molossus) in Gamboa, Panamá, and
 showed that these individuals have low field metabolic rates across a wide
 range of body temperatures that conform to high ambient temperature.
 Importantly, low metabolic rates in controlled respirometry trials were
 best predicted by heart rate, and not body temperature. Molossus molossus
 enter torpor-like states characterized by low metabolic rate and heart
 rates at body temperatures of 32°C, and thermoconform across a range of
 temperatures. Flexible metabolic strategies may be far more common in
 tropical endotherms than currently known.
description: Molossus molossus
 tropical torpor dataRespirometry and
 free-ranging experiment data recording the heart rate (fH, beats per
 minute), body temperature (Tb, °C), and ambient temperature (Ta, °C) for
 Molossus molossus in Gamboa, Panama. Body mass is given in grams.
 Mass-specific energy expenditure (Watts per gram) and field metabolic rate
 (FMR, kJ per day) were measured in flow through respirometry
 only.Molossus tropical torpor data
 JRSO.csv
DOI: 10.5061/dryad.555hd
title: Data from: Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae

description: Chemoautotrophic symbionts of deep sea hydrothermal vent tubeworms are
 known to provide their hosts with all their primary nutrition. While
 studies have examined how chemoautotrophic symbionts provide the
 association with nitrogen, fewer have examined if symbiont nitrogen
 metabolism varies as a function of environmental conditions. Ridgeia
 piscesae tubeworms flourish at Northeastern Pacific vents, occupy a range
 of microhabitats, and exhibit a high degree of morphological plasticity
 [e.g. long-skinny (LS) and short-fat (SF) phenotypes] that may relate to
 environmental conditions. This plasticity affords an opportunity to
 examine whether symbiont nitrogen metabolism varies among host phenotypes.
 LS and SF R. piscesae were recovered from the Axial and Main Endeavour
 Field hydrothermal vents. Nitrate and ammonium were quantified in Ridgeia
 blood, and the expression of key nitrogen metabolism genes, as well as
 stable nitrogen isotope ratios, was quantified in host branchial plume and
 symbiont-containing tissues. Nitrate and ammonium were abundant in the
 blood of both phenotypes though environmental ammonium concentrations
 were, paradoxically, lowest among individuals with the highest blood
 ammonium. Assimilatory nitrate reductase transcripts were always below
 detection, though in both LS and SF R. piscesae symbionts, we observed
 elevated expression of dissimilatory nitrate reductase genes, as well as
 symbiont and host ammonium assimilation genes. Site-specific differences
 in expression, along with tissue stable isotope analyses, suggest that LS
 and SF Ridgeia symbionts are engaged in both dissimilatory nitrate
 reduction and ammonia assimilation to varying degrees. As such, it appears
 that environmental conditions –not host phenotype—primarily dictates
 symbiont nitrogen metabolism.
description: DNA sequences amplified
 by qPCR primersDNA sequences were
 generated by sanger sequencing of amplicons from qPCR
 primersDNA
 sequences.txtqPCR assay
 detailsInformation of qPCR
 assay of standard curves, including R2, efficiency, Ct
 etc.Details
 of qPCR assay.docxReference gene
 evaluationBest reference gene:
 evaluated by NormFinder and GeNormgene expression of reference
 genes for normalization.docxNitrate and ammonia
 concentrationsConcentrations of
 nitrate and ammonia determined in Ridgeia bloodDryad Table_Nitrate and
 ammonium concs.xlsIsotopic
 analysisδ15N of environmental
 nitrate and ammonia, as well as long-skinny and short-fat Ridgeia
 tubewormsFigure 6 isotope
 data.xlsx
DOI: 10.5061/dryad.686sq
title: Data from: Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs

description: The repeated evolution of similar phenotypes by similar mechanisms can be
 indicative of local adaptation, constraints or biases in the evolutionary
 process. Little is known about the incidence of physiological convergence
 in natural populations, so here we test whether energy metabolism in
 ‘dwarf’ and ‘normal’ Lake Whitefish evolves by similar mechanisms. Prior
 genomic and transcriptomic studies have found that divergence in energy
 metabolism is key to local adaptation in whitefish species pairs, but that
 distinct genetic and transcriptomic changes often underlie phenotypic
 evolution among lakes. Here, we predicted that traits at higher levels of
 biological organization, including the activities of energy metabolism
 enzymes (the product of enzyme concentration and turnover rate) and the
 relative proportions of metabolically active tissues (heart, liver,
 skeletal muscle), would show greater convergence than genetic and
 transcriptomic variation. We compared four whitefish species pairs and
 found convergence in organ size whereby all dwarf whitefish populations
 have a higher proportion of red skeletal muscle, three have relatively
 larger livers and two have relatively larger ventricles than normal fish.
 On the other hand, hepatic and muscle enzyme activities showed little
 convergence and were largely dependent on lake of origin. Only the most
 genetically divergent species pair (Cliff Lake) displayed white muscle
 enzyme activities matching results from laboratory-reared normal and dwarf
 whitefish. Overall, these data show convergence in the evolution of organ
 size, but not in the activities of candidate enzymes of energy metabolism,
 which may have evolved mainly as a consequence of demographic or
 ecological differences among lakes.
description: Dalziel_2016_RawDataFile with all raw data and notes on sample collection. Used to calculate residuals or for data transformations if required.Dalziel_2016_26ResponseVariablesFile with data for the 26 response variables used in univariate and multivariate analyses and categorical variables. Residuals are used when variables are significantly correlated with fish mass. If data showed heteroscedasticity we log transformed the response variable or obtained log-log residuals.Dalziel_2016_26ResponseVariablesNumericSame as "Dalziel_2016_26ResponseVariables.csv", but numeric values only to facilitate the creation of the correlation plot (Figure 6) or missing data plot (Figure S1).Dalziel_2016_StandardizedDataFile with standardized data for MANOVA, DFA, PCA. These data can also be calculated from the file "Dalziel_2016_26ResponseVariables.csv" using the R code provided.Dalziel_2016_DFA_ResultsFile with appropriate number of rows (85) for output from DFA (Figure 7) to allow for plots of the first and second linear discriminant.Dalziel_etal_2016_RcodeR code for all data transformations, statistical tests and plots.
DOI: 10.5061/dryad.5s9r5
title: Data from: Temporal and gefitinib-sensitive regulation of cardiac cytokine expression via chronic β-adrenergic receptor stimulation

description: Chronic stimulation of β-adrenergic receptors (βAR) can promote survival
 signaling via transactivation of epidermal growth factor receptor (EGFR),
 but ultimately alters cardiac structure and contractility over time, in
 part via enhanced cytokine signaling. We hypothesized that chronic
 catecholamine signaling will have a temporal impact on cardiac transcript
 expression in vivo, in particular cytokines, and that EGFR transactivation
 plays a role in this process. C57BL/6 mice underwent infusion with vehicle
 or isoproterenol (Iso) ± gefitinib (Gef) for 1 or 2 weeks. Cardiac
 contractility decreased following 2 weeks of Iso treatment, while cardiac
 hypertrophy, fibrosis and apoptosis were enhanced at both timepoints.
 Inclusion of Gef preserved contractility, blocked Iso-induced apoptosis
 and prevented hypertrophy at the 2 week timepoint, but caused fibrosis on
 its own. RNAseq analysis revealed hundreds of cardiac transcripts altered
 by Iso at each timepoint with subsequent RT-qPCR validation confirming
 distinct temporal patterns of transcript regulation, including those
 involved in cardiac remodeling and survival signaling, as well as numerous
 cytokines. While Gef infusion alone did not significantly alter cytokine
 expression, it abrogated the Iso-mediated changes in a majority of the
 βAR-sensitive cytokines, including CCL2 and TNF-α. Additionally, the
 impact of βAR-dependent EGFR transactivation on the acute regulation of
 cytokine transcript expression was assessed in isolated cardiomyocytes and
 in cardiac fibroblasts, where the majority of Iso-dependent, and
 EGFR-sensitive, changes in cytokines occurred. Overall, coincident with
 changes in cardiac structure and contractility, βAR stimulation
 dynamically alters cardiac transcript expression over time, including
 numerous cytokines that are regulated via EGFR-dependent signaling.
description: Grisanti et al. 2014
 Cardiac Transcript DataThis file contains whole
 transcriptome data generated from the hearts of C57BL6/J mice that
 received infusion of the beta adrenergic receptor agonist isoproterenol
 (Iso; 3mg/kg/day) for 1 or 2 weeks. Sheet 1 contains the 1 week Iso versus
 vehicle data and sheet 2 contains the 2 week Iso versus vehicle
 data.
DOI: 10.5061/dryad.c79vc
title: Data from: Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites

description: Coevolution is often invoked as an engine of biological diversity. Avian
 brood parasites and their hosts provide one of the best-known examples of
 coevolution. Brood parasites lay their eggs in the nests of other species,
 selecting for host defences and reciprocal counter-adaptations in
 parasites. In theory, this arms race should promote increased rates of
 speciation and phenotypic evolution. Here we use recently developed
 methods to test whether the three largest avian brood parasitic lineages
 show changes in rates of phenotypic diversity and speciation relative to
 non-parasitic lineages. Our results challenge the accepted paradigm, and
 show that there is little consistent evidence that lineages of brood
 parasites have higher speciation or extinction rates than non-parasitic
 species. However, we provide the first evidence that the evolution of
 brood parasitic behaviour may affect rates of evolution in morphological
 traits associated with parasitism. Specifically, egg size and the colour
 and pattern of plumage have evolved up to nine times faster in parasitic
 than non-parasitic cuckoos. Moreover, cuckoo clades of parasitic species
 that are sympatric (and share similar host genera) exhibit higher rates of
 phenotypic evolution. This supports the idea that competition for hosts
 may be linked to the high phenotypic diversity found in parasitic cuckoos.
description: Trait values per
 speciesTrait values for all the
 species used in the phenotypic rate analyses.all_data_BAMM.xlsColor validationSpectral and RGB measurements for species used in the colour validation analyses.Color_validation.xls