cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b90r6
title: Data from: Why get big in the cold? Size-fecundity relationships explain the temperature-size rule in a pulmonate snail (Physa)

description: Most ectotherms follow a pattern of size plasticity known as the
 temperature-size rule where individuals reared in cold environments are
 larger at maturation than those reared in warm environments. This pattern
 seems maladaptive because growth is slower in the cold so it takes longer
 to reach a large size. However, it may be adaptive if reaching a large
 size has a greater benefit in a cold than in a warm environment such as
 when size-dependent mortality or size-dependent fecundity depends on
 temperature. I present a theoretical model showing how a correlation
 between temperature and the size–fecundity relationship affects optimal
 size at maturation. I parameterize the model using data from a freshwater
 pulmonate snail from the genus Physa. Nine families were reared from
 hatching in one of three temperature regimes (daytime temperature of 22,
 25 or 28 °C, night-time temperature of 22 °C, under a 12L : 12D light
 cycle). Eight of the nine families followed the temperature-size rule
 indicating genetic variation for this plasticity. As predicted, the
 size–fecundity relationship depended upon temperature; fecundity increases
 steeply with size in the coldest treatment, less steeply in the
 intermediate treatment, and shows no relationship with size in the warmest
 treatment. Thus, following the temperature-size rule is adaptive for this
 species. Although rarely measured under multiple conditions,
 size–fecundity relationships seem to be sensitive to a number of
 environmental conditions in addition to temperature including local
 productivity, competition and predation. If this form of plasticity is as
 widespread as it appears to be, this model shows that such plasticity has
 the potential to greatly modify current life-history theory.
description: Physa_Lengths for growth
 trajectoriesIncludes length at ages
 2, 7, 12, 17, 22, 27, 32, and 37 days post-hatching for snails reared in
 three temperature regimes (22, 25, or 28 C) along with family
 designations.Physa_age, size,
 fecundity at maturationIncludes age at
 maturation (days post hatching), length at maturation, and number of eggs
 laid in first brood of snails reared in three temperature regimes (22, 25,
 and 28 C)Physa_adult
 reproductionIncludes total number of
 eggs laid and number of egg masses per day by date for up to 12 broods
 after maturation. Also includes length and wet mass of snails on each of
 those dates. Snails are identified by rearing temperature treatment (22,
 25, or 28 C) and family.
DOI: 10.5061/dryad.m994g
title: Data from: Long-term endemism of two highly divergent lineages of the amphibian-killing fungus in the Atlantic Forest of Brazil

description: The recent global spread of the amphibian-killing fungus [Batrachochytrium
 dendrobatidis (Bd)] has been closely tied to anthropogenic activities;
 however, regional patterns of spread are not completely understood. Using
 historical samples, we can test whether Bd was a spreading or endemic
 pathogen in a region within a particular time frame, because those two
 disease states provide different predictions for the regional demographic
 dynamics and population genetics of Bd. Testing historical patterns of
 pathogen prevalence and population genetics under these predictions is key
 to understanding the evolution and origin of Bd. Focusing on the Atlantic
 Forest (AF) of Brazil, we used qPCR assays to determine the presence or
 absence of Bd on 2799 preserved postmetamorphic anurans collected between
 1894 and 2010 and used semi-nested PCRs to determine the frequency of rRNA
 ITS1 haplotypes from 52 samples. Our earliest date of detection was 1894.
 A mean prevalence of 23.9% over time and spatiotemporal patterns of Bd
 clusters indicate that Bd has been enzootic in the Brazilian AF with no
 evidence of regional spread within the last 116 years. ITS1 haplotypes
 confirm the long-term presence of two divergent strains of Bd (BdGPL and
 Bd-Brazil) and three spatiotemporally broad genetic demes within BdGPL,
 indicating that Bd was not introduced into southeast Brazil by the
 bullfrog trade. Our data show that the evolutionary history and pathogen
 dynamics of Bd in Brazil is better explained by the endemic pathogen
 hypothesis.
description: Spatiotemporal Survey of
 Chytrid in Brazilian Atlantic ForestData from: Long-term
 endemism of two highly divergent lineages of the amphibian-killing fungus
 in the Atlantic Forest of Brazil Authors: Rodriguez, David, Becker,
 Carlos, Pupin, Nadya, Haddad, Célio, Zamudio, Kelly Journal: Molecular
 Ecology Submitted: 2013 File type: ExcelRodriguezetal_MolEco_Dryad_R2.xlsx
DOI: 10.5061/dryad.jn14f
title: Data from: Towards a functional understanding of species coexistence: ecomorphological variation in relation to whole-organism performance in two sympatric lizards

description: 1. We examined intra- and interspecific variation in functional morphology
 and whole-organism performance in a sympatric lizard species pair,
 Iberolacerta horvathi and Podarcis muralis, in the area with a high
 potential for competition. 2. The biggest variation between species was
 found in two functional traits, bite force and climbing speed, linked with
 corresponding morphological traits. 3. The species with larger and taller
 heads, P. muralis, exhibited correspondingly stronger bite forces. The
 other species exhibited smaller and flatter head. Both traits may
 potentially promote segregation between species in trophic niche (stronger
 bites relate to harder prey) and in refuge use (flatter heads allow using
 narrower crevices, hence, influencing escaping from common predators).
 Stronger bites and larger heads also provide one species with a dominant
 position in interspecific agonistic interactions. 4. Females had longer
 trunks that impacted negatively on climbing speed, which may lower
 anti-predator escape abilities of the more trunk-dimorphic species, but
 positively influence reproductive effort. 5. Our results exemplify how the
 joint examination of morphological and functional traits of ecologically
 similar and sympatric species can provide a mechanistic background for
 understanding their coexistence, namely syntopic populations that are
 frequent in the study area. 6. The identified roles of functional
 morphology in this system of sympatric rock lizards support the
 contribution of functional diversification for the complexity of community
 structure via coexistence.
description: Data used to create
 plots and perform all analysisThe data package
 includes the data used to create plots and perform all analysis as detaled
 in the Materials and Methods section of the manuscript. We have examined
 the intra- and interspecific variation in functional morphology and
 whole-organism performance in a sympatric lizard species
 pair.data.csv
DOI: 10.5061/dryad.g1693
title: Data from: Manganese molybdate nanoflakes on silicon microchannel plates as novel nano energetic material

description: Nano energetic materials have attracted great attention recently owing to
 their potential applications for both civilian and military purposes. By
 introducing the silicon microchannel plates (Si-MCPs) three dimensional
 (3D) ordered structure, monocrystalline MnMoO4 with a size of tens of
 micrometers and polycrystalline MnMoO4 nanoflakes are produced on the
 surface and sidewall of the nickel-coated Si-MCP, respectively. The MnMoO4
 crystals ripen controllably forming polycrystalline nanoflakes with the
 lattice fringes of 0.542 nm corresponding to the (1 ̅11) plane on the
 sidewall. And these nanoflakes MnMoO4 shows apparent thermite performance
 which is rarely reported and represents MnMoO4 becomes a new category of
 energetic materials after nanocrystallization. Additionally, the
 nanocrystallization mechanism is interpreted by ionic diffusion caused by
 3D structure. The results indicate that the Si-MCP is a promising
 substrate for nanocrystallization of energetic materials such as MnMoO4.
description: data
 package1 XRD,2 Raman, 3 DSC
 analysisC
 Zhang MnMoO4 Energetic.rar
DOI: 10.5061/dryad.616n0
title: Data from: Evolution of growth by genetic accommodation in Icelandic freshwater stickleback

description: Classical Darwinian adaptation to a change in environment can ensue when
 selection favours beneficial genetic variation. How plastic trait
 responses to new conditions affect this process depends on how plasticity
 reveals to selection the influence of genotype on phenotype. Genetic
 accommodation theory predicts that evolutionary rate may sharply increase
 when a new environment induces plastic responses and selects on sufficient
 genetic variation in those responses to produce an immediate evolutionary
 response, but natural examples are rare. In Iceland, marine threespine
 stickleback that have colonized freshwater habitats have evolved more
 rapid individual growth. Heritable variation in growth is greater for
 marine full-siblings reared at low versus high salinity, and genetic
 variation exists in plastic growth responses to low salinity. In fish from
 recently founded freshwater populations reared at low salinity, the
 plastic response was strongly correlated with growth. Plasticity and
 growth were not correlated in full-siblings reared at high salinity nor in
 marine fish at either salinity. In well-adapted lake populations, rapid
 growth evolved jointly with stronger plastic responses to low salinity and
 the persistence of strong plastic responses indicates that growth is not
 genetically assimilated. Thus, beneficial plastic growth responses to low
 salinity have both guided and evolved along with rapid growth as
 stickleback adapted to freshwater.
description: Archived stickleback
 data rawThis file contains data
 in spreadsheet form on standard length at 150 days post fertilization of
 stickleback from nine replicate Icelandic populations classified into
 three types of population: marine populations, old freshwater lake
 populations and young freshwater lake populations. Full-sib families were
 split with half the progeny reared exclusively at low (5ppt) and half at
 high (35 ppt) salinity. Please see the readme file for details of the data
 structure.
DOI: 10.5061/dryad.rq3ng
title: Data from: Increasing frequency of low summer precipitation synchronizes dynamics and compromises metapopulation stability in the Glanville fritillary butterfly

description: Climate change is known to shift species' geographical ranges,
 phenologies and abundances, but less is known about other population
 dynamic consequences. Here, we analyse spatio-temporal dynamics of the
 Glanville fritillary butterfly (Melitaea cinxia) in a network of 4000 dry
 meadows during 21 years. The results demonstrate two strong, related
 patterns: the amplitude of year-to-year fluctuations in the size of the
 metapopulation as a whole has increased, though there is no long-term
 trend in average abundance; and there is a highly significant increase in
 the level of spatial synchrony in population dynamics. The increased
 synchrony cannot be explained by increasing within-year spatial
 correlation in precipitation, the key environmental driver of population
 change, or in per capita growth rate. On the other hand, the frequency of
 drought during a critical life-history stage (early larval instars) has
 increased over the years, which is sufficient to explain the increasing
 amplitude and the expanding spatial synchrony in metapopulation dynamics.
 Increased spatial synchrony has the general effect of reducing long-term
 metapopulation viability even if there is no change in average
 metapopulation size. This study demonstrates how temporal changes in
 weather conditions can lead to striking changes in spatio-temporal
 population dynamics.
description: Zip-file containing data
 and metadataThis zip-file contains
 several data files - as well as their metadata - that are used for the
 analysesTack et al_2015_PRSB_Archived
 data and metadata.zip
DOI: 10.5061/dryad.n9b7r
title: Data from: Impaired T Cell Responsiveness to Interleukin-6 in Hematological Patients with Invasive Aspergillosis

description: Invasive mold infections (IMI) are among the most devastating
 complications following chemotherapy and hematopoietic stem cell
 transplantation (HSCT), with high mortality rates. Yet, the molecular
 basis for human susceptibility to invasive aspergillosis (IA) and
 mucormycosis remain poorly understood. Herein, we aimed to characterize
 the immune profile of individuals with hematological malignancies (n = 18)
 who developed IMI during the course of chemotherapy or HSCT, and compared
 it to that of hematological patients who had no evidence of invasive
 fungal infection (n = 16). First, we measured the expression of the
 pattern recognition receptors pentraxin 3, dectin-1, and Toll-like
 receptors (TLR) 2 and 4 in peripheral blood of chemotherapy and HSCT
 recipients with IMI. Compared to hematological controls, individuals with
 IA and mucormycosis had defective expression of dectin-1; in addition,
 patients with mucormycosis had decreased TLR2 and increased TLR4
 expression. Since fungal recognition via dectin-1 favors T helper 17
 responses and the latter are highly dependent on activation of the signal
 transducer and activator of transcription (STAT) 3, we next used
 phospho-flow cytometry to measure the phosphorylation of the transcription
 factors STAT1 and STAT3 in response to interferon-gamma (IFN-γ) and
 interleukin (IL)-6, respectively. While IFN-γ/STAT1 signaling was similar
 between groups, naïve T cells from patients with IA, but not those with
 mucormycosis, exhibited reduced responsiveness to IL-6 as measured by
 STAT3 phosphorylation. Furthermore, IL-6 increased Aspergillus-induced
 IL-17 production in culture supernatants from healthy and hematological
 controls but not in patients with IA. Altogether, these observations
 suggest an important role for dectin-1 and the IL-6/STAT3 pathway in
 protective immunity against Aspergillus.
description: Flow Results
 CompiledCompilation of raw data
 from all flow cytometry experiments including surface staining and
 phosphoflow. Sheet 1 is all the data for each patient, Sheet 2 is the log2
 fold change of the MFI used for the heat map (figure 2), Sheet 3 compares
 samples collected &lt;30d after diagnosis vs &gt;30d after diagnosis,
 Sheet 4 examines the effect of freeze-thawing samples on surface staining.
 Statistical analysis on each sheet.ELISA Data (PTX3 IL17
 and IFN)Data from PTX3, IL-17
 and IFN-gamma ELISAs.
DOI: 10.5061/dryad.656gf
title: Data from: Investigation of genetic structure between deep and shallow populations of the southern rock lobster, Jasus edwardsii in Tasmania, Australia

description: The southern rock lobster, Jasus edwardsii, shows clear phenotypic
 differences between shallow water (red coloured) and deeper water (pale
 coloured) individuals. Translocations of individuals from deeper water to
 shallower waters are currently being trialled as a management strategy to
 facilitate a phenotypic change from lower value pale colouration, common
 in deeper waters, to the higher value red colouration found in shallow
 waters. Although panmixia across the J. edwardsii range has been long
 assumed, it is critical to assess the genetic variability of the species
 to ensure that the level of population connectivity is appropriately
 understood and translocations do not have unintended consequences. Eight
 microsatellite loci were used to investigate genetic differentiation
 between six sites (three shallow, three deep) across southern Tasmania,
 Australia, and one from New Zealand. Based on analyses the assumption of
 panmixia was rejected, revealing small levels of genetic differentiation
 across southern Tasmania, significant levels of differentiation between
 Tasmania and New Zealand, and high levels of asymmetric gene flow in an
 easterly direction from Tasmania into New Zealand. These results suggest
 that translocation among Tasmanian populations are not likely to be
 problematic, however, a re-consideration of panmictic stock structure for
 this species is necessary.
description: SRL original genotype
 dataThe Microsoft excel file
 'SRL original genotype data' lists the important data for each
 individual scored in this study. By column, data includes an ID code
 relative to the individual lobster sampled, the site the lobster was taken
 from, the latitude and longitude location of this site, the site code used
 in analysis, the phenotype of the individual, and a list of the 8
 microsatellite genotypes scored for the individual. In columns G to V are
 featured the 8 microsatellite loci, with two columns each indicating each
 allele for the microsatellite. There are 6 sites total sampled across
 Southern Tasmania, and one site sampled in New Zealand (latitude and
 longitude not given for this area).SRL adjusted genotype
 dataThe Microsoft excel file
 'SRL adjusted genotype data' features the same data as that of
 the original file 'SRL original genotype data', excepting that
 the microsatellite data is now represented as it was when adjusted (using
 the number 999) for null alleles. This method involved replacing an
 established number of false homozygote genotypes with the assigned
 heterozygote number of 999. This data set has been indicated as being used
 in some statistical tests, hence may be useful when testing in programs
 that are not robust to the level of null alleles as found in the original
 data set.
DOI: 10.5061/dryad.mf02n
title: Data from: Evidence for a stochastic geometry of biodiversity: the effects of species abundance, richness and intraspecific clustering

description: Most ecological theories that aim to explain coexistence in megadiverse
 communities employ a set of three rules to describe the stochastic
 geometry of biodiversity: (i) individuals exhibit intraspecific
 clustering; (ii) species abundances vary according to a log-normal
 distribution and (iii) the spatial arrangement between species is
 independent. The first two rules have received strong empirical support,
 but the third remains largely unexplored. To address this deficiency, we
 evaluated the independent species arrangement rule in a species-rich
 shrubland and its potential drivers, that is, the levels of species
 richness and intraspecific clustering exhibited by a given species at
 different scales, and the relative abundance of such species in the
 community. We found that interspecific associations were rare and that
 independence was positively related to species richness and intraspecific
 clustering, but negatively related to relative species abundances.
 Synthesis. Our results agree with the independent species arrangement rule
 and they provide empirical support for the stochastic geometry of
 biodiversity. In the context of species-rich plant communities, the
 likelihood of two species encountering is very small. However, our study
 demonstrated a novel feature of this context, where both intraspecific
 clustering (due limitations on dispersal) and relative species abundances
 play fundamental roles in determining the probability of two species
 encountering and interacting, especially at very fine spatial scales.
description: Shrubs
 locationsSpatial coordinates
 corresponding to 7865 individuals belonging to 48 species of perennial
 shrubs and grasses.shrubs_location_JC.xlsx
DOI: 10.5061/dryad.8259
title: Data from: Testicular melanization has evolved in birds with high mtDNA mutation rates

description: Melanin is mainly found in the integument of animals, but it also appears
 in several extracutaneous tissues. The presence of melanin in testes has
 been anecdotally reported in all vertebrate groups, but the causes and
 functions of this melanin remain unknown. Similar to other extracutaneous
 melanins, testicular melanin may protect male germ cells from oxidative
 stress. Given the high respiratory activity of spermatozoa, oxidative
 stress generated by mitochondrial dysfunction as a consequence of mtDNA
 mutations directly affects sperm viability. Thus, natural selection may
 favour testicular melanization in males of species with high historical
 mutation rates in the mitochondrial genome. Here, we tested this
 hypothesis using information on occurrence of testicular melanization and
 mutation accumulation as reflected by cytochrome b mtDNA base pair
 substitution rates in a large set of 134 species of birds, controlling for
 the confounding effects of body mass, reproductive activity and phylogeny.
 We found that testicular melanization has evolved in species with high
 rates of accumulated mitochondrial mutations and propose that this is an
 adaptive response related to the protective capacity of melanin against
 oxidative stress. In support of this hypothesis, testicular melanization
 was more frequently observed during the breeding season of birds (i.e.
 when spermatogenesis is likely to occur) than during reproductive
 inactivity. In contrast to other extracutaneous melanins whose abundance
 seems to reflect skin and coat colour, we did not find a correlation
 between the proportion of plumage coloured by melanins and occurrence of
 testicular melanization. Whereas future experimental studies should test
 these hypotheses, our study highlights for the first time that
 melanization patterns in animals may evolve as a response to historical
 mutation rates.
description: Appendix
 S2Information on
 testicular melanization, body mass (g), mitochondrial DNA substitution
 rate, and eu- and pheomelanin-based plumage coloration in 134 species of
 birds. TM: number of individuals with testicular melanization during the
 breeding and non-breeding seasons, and during periods that could not be
 assigned to any phase of the reproductive cycle (i.e. unknown dates).
 '-' means absence of data for the corresponding reproductive
 phase. Total N: total number of individuals examined. EB: eumelanin-based
 plumage color score. PB: pheomelanin-based plumage color score. Mutation
 rate refers to species-specific mtDNA base pair substitution rate as
 reported by Nabholz et al. (2008, 2009). All data except substitution rate
 are for adult males.Appendix
 S3Phylogenetic hypothesis
 used in the study.
DOI: 10.5061/dryad.g0m3b82
title: Data from: Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers

description: Large-scale empirical evidence indicates a fascinating statistical
 relationship between the estimated number of language users and its
 linguistic and statistical structure. In this context, the linguistic
 niche hypothesis argues that this relationship reflects a negative
 selection against morphological paradigms that are hard to learn for
 adults, since languages with a large number of speakers are assumed to be
 typically spoken and learned by greater proportions of adults. In this
 paper, this conjecture is tested empirically for more than 2,000
 languages. The results question the idea of the impact of non-native
 speakers on the grammatical and statistical structure of languages, as it
 is demonstrated that the relative proportion of non-native speakers does
 not significantly correlate with neither morphological nor
 information-theoretic complexity. While it thus seems that large numbers
 of adult learners/speakers do not affect the (grammatical or statistical)
 structure of a language, the results suggest that there is indeed a
 relationship between the number of speakers and (especially)
 information-theoretic complexity, i.e. entropy rates. A potential
 explanation for the observed relationship is discussed.
description: Data table to reproduce
 all resultsdata_table.xlsxStata_filesStata 14 code to reproduce all results