cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.878q6
title: Data from: Factors affecting N-nitrosodimethylamine formation from poly(diallyldimethyl-ammonium chloride) degradation during chloramination

description: Poly (diallyldimethyl ammonium chloride) (polyDADMAC) has been shown to be
 an important precursor of the probable human carcinogen
 N-nitrosodimethylamine (NDMA) when in contact with chloramine. In this
 study, we conducted an orthogonal experiment design to evaluate the
 effects of pH values, ammonia, bromide, natural organic matter (NOM) and
 monochloramine dosages on the formation of NDMA from polyDADMAC during
 chloramination. Meanwhile, single factor experiments of pH, bromide and
 NOM prove the results of orthogonal experiment. The results supported that
 pH was the most critical factor affecting NDMA formation from polyDADMAC
 during the chloramines, and the highest NDMA formation from polyDADMAC
 occurred near pH at 7 due to released DMA from polyDADMAC degradation and
 the critical importance of low concentrations of dichloramine in water. In
 the presence of excess bromide, the NDMA formation was enhanced
 significantly at all different pH values owing to bromochloramine, which
 has higher electronegativity of the brominated nitrogen atom than
 monochloramine or dichloramine. The NDMA formation from polyDADMAC in the
 presence of NOM was 41.7% lower than NDMA formation in absence of NOM. The
 overwhelming majority of NDMA formation from polyDADMAC under stimulated
 conditions were lower than the current advisory levels (i.e., 9 ng/L in
 Ontario, 10 ng/L in California).
description: RawdataThe raw data for Figure 2,3,4 and 6.
DOI: 10.5061/dryad.6394c
title: Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'

description: Recent higher-level frog phylogenetic analyses have included a few members
 of the endemic Philippine frog genus Sanguirana. Although the monophyly of
 the group has never been disputed, the recent phylogenetically-supported
 inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade
 was highly unexpected. In addition, species boundaries and relationships
 remain unclear and new species continue to be discovered. We estimate the
 phylogeny for this endemic Philippine genus using two mitochondrial gene
 regions and six nuclear loci and complete sampling for all known species.
 We use a time-calibrated Bayesian estimate of phylogeny and model-testing
 approach to biogeographic inference to infer ancestral areas and probable
 means of diversification. These analyses identify Sanguirana as an
 additional clade for which the biogeographic ‘Out-of-Palawan’
 biogeographic scenario is unambiguously preferred. This study lends
 additional support to recent work suggesting that a substantial portion of
 Philippine vertebrate megadiversity originated via colonization of the
 archipelago from the Palawan microcontinent, with subsequent invasion of
 oceanic islands (e.g., range expansion over Huxley’s Modification of
 Wallace’s Line), numerous instances of overwater dispersal, and geographic
 radiation across the archipelago.
description: Results of tree
 analysesMrBayes results: (1)
 mt+nc combined matrix and tree (161 samples); (2) mt matrix and tree (161
 samples); and (3) nc matrix and tree (59 samples). BEAST results using
 reduced matrices (51 samples): (1) molecular clock calibrated tree and (2)
 geological event calibrated tree. RAxML result using reduced
 matrix.submit to
 Dryad.zip
DOI: 10.5061/dryad.h5j86
title: Data from: Impacts of warming revealed by linking resource growth rates with consumer functional responses

description: Warming global temperatures are driving changes in species distributions,
 growth and timing, but much uncertainty remains regarding how climate
 change will alter species interactions. Consumer-Resource interactions in
 particular can be strongly impacted by changes to the relative performance
 of interacting species. While consumers generally gain an advantage over
 their resources with increasing temperatures, nonlinearities can change
 this relation near temperature extremes. We use an experimental approach
 to determine how temperature changes between 5 and 30 °C will alter the
 growth of the algae Scenedesmus obliquus and the functional responses of
 the small bodied Daphnia ambigua and the larger D. pulicaria. The impact
 of warming generally followed expectations, making both Daphnia species
 more effective grazers, with the increase in feeding rates outpacing the
 increases in algal growth rate. At the extremes of our temperature range,
 however, warming resulted in a decrease in Daphnia grazing effectiveness.
 Between 25 and 30°C both species of Daphnia experienced a precipitous drop
 in feeding rates, while algal growth rates remained high, increasing the
 likelihood of algal blooms in warming summer temperatures. D. pulicaria
 performed significantly better at cold temperatures than D. ambigua, but
 by 20°C there was no significant difference between the two species and at
 25°C D. ambigua out-performed D. pulicaria. Warming summer temperatures
 will favor the smaller D. ambigua, but only over a narrow temperature
 range and warming beyond 25°C could open D. ambigua to invasion from
 tropical species. By fitting our results to temperature dependent
 functions we develop a temperature and density dependent model which
 produces a metric of grazing effectiveness, quantifying the grazer density
 necessary to halt algal growth. This approach should prove useful for
 tracking the transient dynamics of other density dependent
 consumer-resource interactions, such as agricultural pests and biological
 control agents.
description: Algal growth time
 seriesDensity of algal
 cultures through time across 6 different temperaturesAlgal
 density.xlsFunctional Response
 dataResults of the
 functional response experiments. For each replicate the species, number of
 Daphnia, time elapsed in the feeding trial, initial density of Scenedesmus
 obliquus and final density of S. obliquus is provided.
DOI: 10.5061/dryad.8fc60
title: Data from: Population growth in a wild bird is buffered against phenological mismatch

description: Broad-scale environmental changes are altering patterns of natural
 selection in the wild, but few empirical studies have quantified the
 demographic cost of sustained directional selection in response to these
 changes. We tested whether population growth in a wild bird is negatively
 affected by climate change–induced phenological mismatch, using almost
 four decades of individual-level life-history data from a great tit
 population. In this population, warmer springs have generated a mismatch
 between the annual breeding time and the seasonal food peak, intensifying
 directional selection for earlier laying dates. Interannual variation in
 population mismatch has not, however, affected population growth. We
 demonstrated a mechanism contributing to this uncoupling, whereby fitness
 losses associated with mismatch are counteracted by fitness gains due to
 relaxed competition. These findings imply that natural populations may be
 able to tolerate considerable maladaptation driven by shifting climatic
 conditions without undergoing immediate declines.
description: Individual and
 population level great tit dataComma-separated values
 data file containing individual level and population level great tit data
 from the Hoge Veluwe study site, the Netherlands. Explanation of the
 variables included in the file
 "parus_maj_MS_code.R"parus_maj_data.csvparus_maj_MS_codeR code to run the analyses presented in the paper (including those in the supplementary online material). Also code to produce the graphs in the paper. Additional functions used in the code are provided in the file 'my.functions.R'.my functionsCustomized functions used in the main R code analyses and simulations.Projected mismatchProjected future values of population mismatch under different climate change scenarios. Used as input in the simulation model.projectedMM.csvparus_maj_simulationR code to run the simulation model presented in the paper. Code is fully commented with instructions and explanations.
DOI: 10.5061/dryad.1960
title: Data from: Constraints on speciation suggested by comparing lake-stream stickleback divergence across two continents

description: Adaptation to ecologically distinct environments can coincide with the
 emergence of reproductive barriers. The outcome of this process is highly
 variable and can range along a continuum from weak population
 differentiation all the way to complete, genome-wide divergence. The
 factors determining how far diverging taxa will move along this continuum
 remain poorly understood but are most profitably investigated in taxa
 under replicate divergence. Here we explore determinants of progress
 toward speciation by comparing phenotypic and molecular divergence within
 young (&lt; 150 years) lake-stream stickleback pairs from Central
 Europe to divergence in older (thousands of years) archetypal lake-stream
 pairs from Vancouver Island, Canada. We generally find relatively weak
 divergence in most aspects of foraging morphology (gill raker number, body
 shape) in the European pairs, although substantial adaptive divergence is
 seen in gill raker length. Combined with striking overall phenotypic
 differences between the continents, this argues for genetic and time
 constraints on adaptive divergence in the European pairs. The European
 lake-stream pairs also do not display the strong habitat-related
 differentiation in neutral (microsatellite) markers seen in the Canadian
 watersheds. This either indicates the lack of strong reproductive barriers
 owing to weak adaptive divergence, or alternatively, that neutral markers
 are poorly suited for detecting reproductive barriers if these emerge
 rapidly. Overall, our comparative approach suggests constraints on
 speciation due to genetic architecture and limited time for divergence.
 The relative importance of these factors remains to be quantified by
 future investigation.
description: microsatellite data
 Berner et al. 2010morphology data Berner
 et al. 2010
DOI: 10.5061/dryad.510sb
title: Data from: Identifying future zoonotic disease threats: where are the gaps in our understanding of primate infectious diseases?

description: Background and objectives: Emerging infectious diseases often originate in
 wildlife, making it important to identify infectious agents in wild
 populations. It is widely acknowledged that wild animals are incompletely
 sampled for infectious agents, especially in developing countries, but it
 is unclear how much more sampling is needed, and where that effort should
 focus in terms of host species and geographic locations. Here we identify
 these gaps in primate parasites, many of which have already emerged as
 threats to human health. Methodology: We obtained primate host-parasite
 records and other variables from existing databases. We then investigated
 sampling effort within primates relative to their geographic range size,
 and within countries relative to their primate species richness. We used
 generalized linear models, controlling for phylogenetic or spatial
 autocorrelation, to model variation in sampling effort across primates and
 countries. Finally, we used species richness estimators to extrapolate
 parasite species richness. Results: We found uneven sampling effort within
 all primate groups and continents. Sampling effort among primates was
 influenced by their geographic range size and substrate use, with
 terrestrial species receiving more sampling. Our parasite species richness
 estimates suggested that, among the best-sampled primates and countries,
 almost half of primate parasites remain to be sampled; for most primate
 hosts, the situation is much worse. Conclusions and implications: Sampling
 effort for primate parasites is uneven and low. The sobering message is
 that we know little about even the best studied primates, and even less
 regarding the spatial and temporal distribution of parasitism within
 species.
description: Cooper&Nunn_CountryParasiteSACThis contains the data needed to plot parasite species accumulation curves for each countryCooper&Nunn_PhylogeneticModelsThis contains the data needed to identify well- and poorly-sampled primate species in relation to their geographic range. And also the data needed to fit models of sampling events against primate characteristics.Cooper&Nunn_GeographicalModelsThis contains the data needed to identify well- and poorly-sampled countries in relation to their primate species richness. And also the data needed to fit models of sampling events against country characteristics.Cooper&Nunn_CountryParasiteSACThis contains the data needed to plot parasite species accumulation curves for each country
DOI: 10.5061/dryad.271dk
title: Data from: DBGC: a database of human gastric cancer

description: The Database of Human Gastric Cancer (DBGC) is a comprehensive database
 that integrates various human gastric cancer-related data resources. Human
 gastric cancer-related transcriptomics projects, proteomics projects,
 mutations, biomarkers and drug-sensitive genes from different sources were
 collected and unified in this database. Moreover, epidemiological
 statistics of gastric cancer patients in China and clinicopathological
 information annotated with gastric cancer cases were also integrated into
 the DBGC. We believe that this database will greatly facilitate research
 regarding human gastric cancer in many fields. DBGC is freely available at
 http://bminfor.tongji.edu.cn/dbgc/index.do
description: DBGC: A Database of
 Human Gastric CancerOur work collected the
 data from transcriptome, proteome, mutation, biomarker and drug-sensitive
 genes. Totally comes out 9 files: 1，transcriptome.txt -- transcriptome
 related to gastric cancer, that contains the type of experiment, platform,
 sample, volume, result and the linkage of those. 2，up_genes.txt --
 up-regulated gene list come from transcriptome which based on experiment
 3，down_genes.txt -- up-regulated gene list come from transcriptome which
 based on experiment 4，proteome.txt -- proteome related to gastric cancer,
 that contains the type of experiment, sample, technology and result etc.
 5，up_proteins.txt -- up-regulated genes list come from proteome
 6，down_proteins.txt -- down-regulated genes list come from proteome
 7，mutation.txt -- mutation related to gastric cancer, that mainly include
 mutation type, postion etc. 8，biomarker.txt -- biomarker related to
 gastric cancer including types, stages as well sensitivity, specifity ect.
 9，pharmacogenomics.txt -- include gastric cancer gene and drug detail as
 well as resistance mechanism etcdbgc.rar
DOI: 10.5061/dryad.2dm26
title: Data from: Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from Kenya.

description: The mosquito midgut is a hostile environment that vector-borne parasites
 must survive in order to be transmitted. Commensal bacteria in the midgut
 can reduce the ability of mosquitoes to transmit disease, either by having
 direct anti-parasite effects or by stimulating basal immune responses of
 the insect host. As different bacteria have different effects on parasite
 development, the composition of the bacterial community in the mosquito
 gut is likely to affect the probability of disease transmission. We
 investigated the diversity of mosquito gut bacteria in the field using 454
 pyrosequencing of 16S rRNA to build up a comprehensive picture of the
 diversity of gut bacteria in 8 mosquito species. We found that mosquito
 gut typically has a very simple gut microbiota that is dominated by a
 single bacterial taxon. Although different mosquito species share
 remarkably similar gut bacteria, individuals in a population are extremely
 variable and can have little overlap in the bacterial taxa present in
 their guts. This may be an important factor in causing differences in
 disease transmission rates within mosquito populations.
description: OTUsMultiple alignment of
 filtered and annotated bacterial 16S based OTUs.Osei_Poku2012_OTUs.fasta
DOI: 10.5061/dryad.g23s038
title: Data from: The specificity of Burkholderia symbionts in the social amoeba farming symbiosis: prevalence, species, genetic and phenotypic diversity

description: The establishment of symbioses between eukaryotic hosts and bacterial
 symbionts in nature is a dynamic process. The formation of such
 relationships depends on the life history of both partners. Bacterial
 symbionts of amoebae may have unique evolutionary trajectories to the
 symbiont lifestyle, because bacteria are typically ingested as prey. To
 persist after being eaten, bacteria must survive phagocytosis. In the
 social amoeba Dictyostelium discoideum, certain strains of Burkholderia
 bacteria are able to resist amoebal digestion and maintain a persistent
 relationship that includes carriage throughout the amoeba’s social cycle
 that culminates in spore formation. Some Burkholderia strains allow their
 host to carry other bacteria as food. This carried food is released in new
 environments in a trait called farming. To better understand the diversity
 and prevalence of Burkholderia symbionts and the traits they impart to
 their amoebae hosts, we first screened 700 natural isolates of D.
 discoideum and found 25% infected with Burkholderia. We next used a
 multilocus phylogenetic analysis and identified two independent
 transitions by Burkholderia to the symbiotic lifestyle. Finally, we tested
 the ability of 38 strains of Burkholderia, from D. discoideum and as well
 as strains isolated from other sources, for traits relevant to symbiosis
 in D. discoideum. Only D. discoideum native isolates belonging to the B.
 agricolaris, B. hayleyella, and B.bonniea species were able to form a
 persistent symbiotic association with D. discoideum. The Burkholderia
 Dictyostelium relationship provides a promising arena for further studies
 of the pathway to symbiosis in a unique system.
description: Figure 1 data -
 Burkholderia prevalenceThis is an excel data
 file with the Burkholderia prevalence in D. discoideum used to create
 figure 1. It show the number of D. discoideum sampled from each location
 and the identity of the Burkholderia.Figure1_BurkholderiaPrevalenceScreening.xlsFigure 3 data - MLST traitsExcel file used to generate the symbiotic trait figure. This includes Burkholderia species and strain, and the scaling for each trait.Figure3_MLST.Traits.xlsxFigure6_SporeProductivityThis excel file contains the sport counting data for each Burkholderia infected D. discoideum clone.BurkholderiaMLSAconcatenatedALNThis is a fasta file that contains the concatenated alignment for all Burkholderia strains in this study.
DOI: 10.5061/dryad.853t3
title: Data from: Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the Last Glacial Maximum in the southern Andean beech forests

description: Historical climate changes and orogenesis are two important factors that
 have shaped intraspecific biodiversity patterns worldwide. Although
 southern South America has experienced such complex events, there is a
 paucity of studies examining the effects on intraspecific diversification
 in this part of the world. Liolaemus pictus is the southernmost
 distributed lizard in the Chilean temperate forest, whose genetic
 structure has likely been influenced by Pleistocene glaciations. We
 conducted a phylogeographic study of L. pictus in Chile and Argentina
 based on one mitochondrial and two nuclear genes, and recovered two
 strongly divergent groups, Northern and Southern clades, the former
 distributed from the northernmost limit of the species to the Araucanía
 region, and the latter being distributed throughout the Andes and the
 Chiloé archipelago in Southern Chile. Our results suggest that L. pictus
 originated 751 Kya, with divergence between the two clades occurring in
 the late Pleistocene. Demographic reconstructions for the Northern and
 Southern clades indicate a decrease in effective population sizes likely
 associated with Pleistocene glaciations. Surprisingly, patterns of genetic
 variation, clades ages and historical gene flow in populations distributed
 within the limits of the Last Glacial Maximum (LGM) are not explained by
 recent colonization. We propose an “intra-Andean multiple refuge”
 hypothesis, along with the classical refuge hypothesis previously proposed
 for the biota of the Chilean Coastal range and Eastern Andean Cordillera.
 Our hypothesis is supported by niche modeling analysis suggesting the
 persistence of fragments of suitable habitat for the species within the
 limits of the LGM ice shield. This type of refuge hypothesis is proposed
 for the first time for an ectothermic species.
description: Lpictus con
 2OGFasta file of all the
 mtDNA sequences used to run phylogeographic analyses on JModeltest, Bayes
 Phylogenies, TCS, Mega and DNAsp.GenelandData used to run Geneland. The file includes coordinates and sequences. Nucleobases were changed by numbers (1-4) in order to be able to run Geneland.SecuenciasEXPH5GenBank_oKSequences for the nuclear gene EXPH5. Alleles at heterozygous sites were inferred with PHASE 2.1SecuenciasLDB5B_GenBankSequences from the nuclear gene LDB5B. Alleles at heterozygous sites were inferred with PHASE 2.1LpictusSeqNoGapAISInput file for the software Alleles In Space
DOI: 10.5061/dryad.c95fk
title: Data from: Extreme diel dissolved oxygen and carbon cycles in shallow vegetated lakes

description: A common perception in limnology is that shallow lakes are homogeneously
 mixed owing to their small water volume. However, this perception is
 largely gained by downscaling knowledge from large lakes to their smaller
 counterparts. Here we show that shallow vegetated lakes (&lt; 0.6 m),
 in fact, undergo recurring daytime stratification and nocturnal mixing
 accompanied by extreme chemical variations during summer. Dense submerged
 vegetation effectively attenuates light and turbulence generating
 separation between warm surface waters and much colder bottom waters.
 Photosynthesis in surface waters produces oxygen accumulation and CO2
 depletion, whereas respiration in dark bottom waters causes anoxia and CO2
 accumulation. High daytime pH in surface waters promotes precipitation of
 CaCO3 which is re-dissolved in bottom waters. Nocturnal convective mixing
 re-introduces oxygen into bottom waters for aerobic respiration and
 regenerated inorganic carbon into surface waters, which supports intense
 photosynthesis. Our results reconfigure the basic understanding of local
 environmental gradients in shallow lakes, one of the most abundant
 freshwater habitats globally.
description: source_dataData for figure 1-5 and supplementary figure 1-2