cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18q5n
title: Data from: How temporal patterns in rainfall determine the geomorphology and carbon fluxes of tropical peatlands

description: Tropical peatlands now emit hundreds of megatons of carbon dioxide per
 year because of human disruption of the feedbacks that link peat
 accumulation and groundwater hydrology. However, no quantitative theory
 has existed for how patterns of carbon storage and release accompanying
 growth and subsidence of tropical peatlands are affected by climate and
 disturbance. Using comprehensive data from a pristine peatland in Brunei
 Darussalam, we show how rainfall and groundwater flow determine a shape
 parameter (the Laplacian of the peat surface elevation) that specifies,
 under a given rainfall regime, the ultimate, stable morphology, and hence
 carbon storage, of a tropical peatland within a network of rivers or
 canals. We find that peatlands reach their ultimate shape first at the
 edges of peat domes where they are bounded by rivers, so that the rate of
 carbon uptake accompanying their growth is proportional to the area of the
 still-growing dome interior. We use this model to study how tropical
 peatland carbon storage and fluxes are controlled by changes in climate,
 sea level, and drainage networks. We find that fluctuations in net
 precipitation on timescales from hours to years can reduce long-term peat
 accumulation. Our mathematical and numerical models can be used to predict
 long-term effects of changes in temporal rainfall patterns and drainage
 networks on tropical peatland geomorphology and carbon storage.
description: Soil surface CO2 flux
 dataComma-separated text
 table containing daily averages of barometrically corrected water table
 height and soil surface CO2 flux, as described in the "Soil
 respiration" section of the SI Methods. These data appear in Figure
 4b of the paper.Cobb_et_al_co2_flux_data.txtRadiocarbon dates from peat samplesComma-separated text table containing calibrated radiocarbon dates from peat samples, shown in Figure 7 of the paper. Of the data in the table, 22 the dates from 7 cores first appeared in Gandois et al. (2014), and 7 dates from 1 core first appeared in Dommain et al. (2015), in addition to the 6 dates from 1 core first appearing here, as noted in the "Source" column of the table.Cobb_et_al_radiocarbon_data.txtREADME for data filesText file explaining data package files and their fields. Also provides acknowledgements and contact information.
DOI: 10.5061/dryad.10bb924
title: Data from: Response of ants to human-altered habitats with reference to seed dispersal of Corydalis giraldii Fedde (Papaveraceae)

description: Anthropogenic habitat disturbance has potential consequences for ant
 communities. However, there is limited information on the effects of ant
 responses on associated ecological processes such as seed dispersal. We
 investigated the effect of disturbance on the abundance, richness, and
 composition of ant communities and the resulting seed‐dispersal services
 for a herbaceous myrmecochore, Corydalis giraldii (Papaveraceae), in an
 undisturbed habitat (forest understory), moderately disturbed habitat
 (abandoned farm field), and highly disturbed habitat (road verge) on
 Qinling Mountains, China. In total, we recorded 13 ant species, and five
 out of these were observed to transport seeds. The community composition
 of dispersers was significantly different amongst habitats. The richness
 of the dispersers did not differ among the habitats, but their total
 abundance significantly varied across habitats and was recorded to
 decrease in the road verge by 21%, in comparison to abandoned farm fields.
 The major seed‐dispersing ant species in both the forest understory and
 abandoned farm field were large‐bodied (Myrmica sp. and Formica fusca,
 respectively), whereas the major seed‐dispersing ants found in the road
 verge were small‐bodied (Lasius alienus). This difference resulted in
 lower seed removal rates and dispersal distances in the road verge than in
 the other two habitats. The different dispersal patterns were attributed
 primarily to differences in dispersing ant abundance and identity, most
 likely in response to habitats with different degree of anthropogenic
 disturbance. The possible influence of disturbance on the ecological
 specialization of ant‐seed dispersal interaction was also discussed.
description: Raw data for seed
 dispersalRaw
 data.xlsx
DOI: 10.5061/dryad.1r59s
title: Data from: Effects of arbuscular mycorrhizal fungi on aboveground tri-trophic interactions are contingent upon plant genetic effects of cross type in the perennial herb Ruellia nudiflora

description: 1.- Recent work has improved our understanding of the linkages between
 above- and below-ground interactions mediated by plants. However,
 relatively few of the studies conducted thus far have focused on
 muli-trophic interactions (i.e. beyond two trophic levels) and the
 influence of plant genetic intra-specific variation on these dynamics has
 rarely been addressed. 2.- We tested the effect of arbuscular mycorrhizal
 fungi (AMF) on above-ground tri-trophic interactions associated with the
 canopy of the perennial herb Ruellia nudiflora, and further determined
 whether genetic effects due to cross type (i.e. wether a plant originated
 from from self- or cross-pollination) influenced these interactions. 3.-
 We propagated plants originating from self- or cross-pollination, and
 within each category inoculated half of the plants with AMF. We
 subsequently established a common garden where plants were exposed to
 naturally occurring seed-eating caterpillars and their parasitoids. We
 measured plant growth, fruit output, calculated the proportion of attacked
 fruits by the caterpillar and the proportion of parasitized caterpillars,
 and also estimated the proportion of “rescued” seeds by parasitoids
 representing an indirect positive effect of the third trophic level on the
 plant by reducing caterpillar consumption. 4.- AMF drove 18% and 15%
 increases in plant growth and fruit output respectively, and drove a 25%
 reduction in caterpillar fruit attack, but did not influence parasitism or
 parasitoid seed “rescue”. In contrast, cross type did not influence
 growth, fruit number, herbivore attack, parasitism, or seed rescue. More
 importantly, however, we found a significant AMF by cross type interaction
 on caterpillar attack where AMF significantly reduced fruit attack (by
 30%) in progeny from cross-pollination but did not influence herbivory in
 progeny from self-pollination. 5.- Synthesis. Results indicate that AMF
 effects on above-ground interactions are contingent upon plant
 intra-specific variation originating from cross type, which is likely a
 common source of variation in associated interactions for plants with
 mixed mating systems. Further studies examining plant-mediated below- and
 aboveground interactions should consider the influence of specific sources
 of plant genetic variation, as well as address the consequences of such
 dynamics for interactions beyond two trophic levels.
description: DataMejia-AlvaetalThe data were collected in the field from July 2014 to January 2015 in plots of Campus de Ciencia Biológicas y Agropcuarias of the Universidad Autónoma de Yucatán, México. Abbreviated headlines are as follows: “Plant” = Plant identity; “Fam” = Genetic family; “AMF” = WITH AMF, WITHOUT AMF; “CT” = Cross type; ”Fruit” = Number of fruits; “Prop.Attack” = Proportion of fruits attacked; “Prop.P” = Proportion of fruits with parasitoids; “Cover” = Plant cover
DOI: 10.5061/dryad.1172
title: Data from: The effects of temporal resolution on species turnover and on testing metacommunity models

description: Patterns of low temporal turnover in species composition found within long
 paleoecological time series contrast with the high turnover predicted by
 dispersal-limited neutral metacommunity models and thus have been used to
 support non-neutral models. However, predictions assume temporal
 resolution on the scale of a season or year whereas individual fossil
 assemblages are typically time-averaged to decadal or centennial time
 scales. Here, we simulate the effects of time averaging by building
 time-averaged assemblages from local dispersal-limited non-averaged
 (living) assemblages and compare the predicted species turnover with
 observed patterns in mollusk and ostracod fossil records. Time averaging
 substantially reduces temporal turnover such that neutral predictions
 converge with those of trade-off and density-dependent models, and tends
 to decrease species dominance and increase the proportion of rare species.
 Observed turnover rates are comparable to an appropriately scaled neutral
 model: patterns of high community stability can be produced or reinforced
 by time averaging alone. The community attributes of local time-averaged
 assemblages approach those of the metacommunity. Time-averaged assemblages
 are thus unlikely to capture attributes arising from processes operating
 at small spatial scales, but should do well at capturing the turnover and
 diversity parameters of metacommunities, and thus will be a valuable basis
 for analyzing the large-scale processes that determine metacommunity
 evolution.
description: Tanganyika-SADs of
 metacommunities.RdataFive vectors with
 simulated abundances of individual ostracod species for the Lake
 Tanganyika in neutral metacommunities differing in the migration rates (m
 = 0.005, m = 0.05, m = 0.145, m = 0.25, m = 0.5). Format: .Rdata files for
 R-languageCopano Bay cores
 data.txtAbsolute abundances of
 mollusks in two sediment cores sampled by sieving in the Copano Bay. Core
 1 - C1 is represented by nine layers. Core 2 - C2 is represented by 14
 layers. Core 1 was simulated in Tomasovych and Kidwell 2010. Format:
 tab-delimited txt.file. The source citation for these data and details
 about sampling are in: Powell, E. N., and R. J. Stanton, Jr. 1995. The
 application of guild and tier structure and energy flow in paleoecologic
 analysis: an example using parautochthonous death assemblages from a
 variable salinity bay. Historical Biology 10:281-327.Powell, E. N., and R.
 J. Stanton, Jr. 1996. The application of size-frequency distribution and
 energy flow in paleoecologic analysis: an example using parautochthonous
 death assemblages from a variable salinity bay. Palaeogeography
 Palaeoclimatology Palaeoecology 124:195-231.Copano-SADs of
 metacommunities.RdataFive vectors with
 simulated abundances of individual ostracod species for the Lake
 Tanganyika in neutral metacommunities differing in the migration rates (m
 = 0.005, m = 0.05, m = 0.145, m = 0.25, m = 0.5). Format: .Rdata files for
 R-language
DOI: 10.5061/dryad.dr78n
title: Data from: Auditory threshold shifts after glycerol administration to patients with suspected Menière's disease: a retrospective analysis

description: Objectives: Nearly half a century ago, administration of glycerol was
 shown to temporarily improve the threshold of hearing in patients with
 suspected Menière's disease (glycerol test). Although a positive test
 result provides strong evidence of Menière's disease, the test has
 not gained widespread acceptance. A probable reason is that there is no
 consensus as to the definition of positive. Moreover, a negative test
 result is of little diagnostic value because Menière's disease cannot
 be excluded. By reanalyzing archived data, the authors sought to
 understand the test in light of signal detection theory. Moreover, they
 explored the possibility of estimating the probability of a positive test
 result from the pretest audiogram. Design: The study is based on
 audiograms from 347 patients (356 ears) who underwent a glycerol test to
 corroborate a suspected diagnosis of Menière's disease. Subsequent to
 an initial pure-tone audiogram, glycerol (1.2 mL/kg body weight) was
 orally administered; follow-up audiograms were obtained after 1, 2, 3, and
 4 hr. Transcription of the audiograms into a computer-readable form made
 them available for automated reanalysis. Results: Averaged difference
 audiograms provided detailed insight into the frequency dependence and the
 temporal dynamics of the glycerol-induced threshold reduction. The
 strongest threshold reduction was observed 4 hr after glycerol intake,
 although nearly the same effect was already found after 3 hr. Strong
 overall threshold reductions were associated with a pronounced maximum at
 approximately 1000 Hz; weaker effects were associated with a plateau
 between 125 and 1000 Hz and a rapid decrease toward higher frequencies. To
 date, criteria suggested for a positive test result vastly differ in both
 sensitivity (with regard to the detection of a threshold reduction) and
 specificity (1 minus false-positive rate). Here, a criterion based on the
 aggregate threshold reduction in adjacent audiometric frequencies is
 suggested. This approach does not only seem to be more robust but also
 permits to freely adjust the false-positive rate. A positive test result
 is particularly likely when the mean low-frequency hearing loss is
 approximately 60 dB and the mean high-frequency hearing loss does not
 exceed 50 dB. Conclusion: If the pretest audiogram does not render a
 positive test result unlikely, a state-of-the-art implementation of the
 glycerol test is a competitive method for corroborating a suspected
 diagnosis of Menière's disease.
description: Data of the Ear &
 Hearing article (2013) by Basel and LütkenhönerThe zip-file contains
 the data of a retrospective analysis of the glycerol test in patients with
 suspected Menière's disease (356 ears). Moreover, a MATLAB script
 exemplifes how to use the data.data_BaselLutkenhoner2013.zip
DOI: 10.5061/dryad.06g5v
title: Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation

description: Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas
 archipelago from Patagonia in the 1930s. After introduction, the Guanaco
 population increased to almost 400 animals that retained a footprint of
 the founding effect and bottleneck reflected in the genetic status of this
 isolated population. The goals of this study were to (i) make a genetic
 assessment of this island population through comparisons with mainland
 populations and simulation, and (ii) assess the likely source population
 of the introduced Guanacos. Genetic variation estimated from 513 bp of
 mitochondrial DNA sequence and 15 microsatellite loci were compared among
 154 Guanacos collected from eight localities, including the adjacent
 mainland and the islands of Tierra del Fuego and Staats Island. Of the 23
 haplotypes observed among our samples, the Staats Island population only
 contained three haplotypes, all of which were shared with the Monte Leon
 population in southern Patagonia. Mitochondrial DNA and microsatellite
 variation on Staats Island were comparable to most mainland populations
 and greater than those observed on Tierra del Fuego. Patterns of genetic
 structure suggest that the Staats Island Guanaco population was founded
 with animals from southern Patagonia (as opposed to northern Patagonia or
 Tierra del Fuego), but that effective reductions in population size lasted
 only a few generations and that surviving animals were a random sample of
 the pre-bottleneck genetic variation.
description: MicrosatGuanacosFalkland24-7-09bMicrosatellities data
DOI: 10.5061/dryad.3r8n6
title: Data from: Two-current choice flumes for testing avoidance and preference in aquatic animals

description: Aquatic chemical ecology is an important and growing field of research
 that involves understanding how organisms perceive and respond to chemical
 cues in their environment. Research assessing the preference or avoidance
 of a water source containing specific chemical cues has increased in
 popularity in recent years, and a variety of methods have been described
 in the scientific literature. Two-current choice flumes have seen the
 greatest increase in popularity, perhaps because of their potential to
 address the broadest range of research questions. Here, we review the
 literature on two-current choice flumes and show that there is a clear
 absence of standardized methodologies that make comparisons across studies
 difficult. Some of the main issues include turbulent flows that cause
 mixing of cues, inappropriate size of choice arenas for the animals, short
 experiments with stressed animals, failure to report how experiment and
 researcher biases were eliminated, general underreporting of
 methodological details, underutilization of collected data and
 inappropriate data analyses. In this review, we present best practice
 guidelines on how to build, test and use two-current choice flumes to
 measure the behavioural responses of aquatic animals to chemical cues, and
 provide blueprints for flume construction. The guidelines include steps
 that can be taken to avoid problems commonly encountered when using
 two-current choice flumes and analysing the resulting data. This review
 provides a set of standards that should be followed to ensure data
 quality, transparency and replicability in future studies in this field.
description: Data for Jutfelt et al.
 Figure 7Figure 7. Side
 preferences (1 min means) of two humbug damselfish (Dascyllus aruanus)
 over time. The first 38 minutes in the flume are without cue (note the
 different side preferences in the two individuals), then 20 minutes with a
 predator cue down one side of the flume (side A), and finally a side
 switch at 58 minutes before another 20 minutes with the predator cue down
 the opposite side (side B). The grey shaded areas indicate the side of the
 flume containing predator cue.Jutfelt et al Choice Flume
 review data figure 7.xlsx
DOI: 10.5061/dryad.70fg7
title: Data from: The evolution of coexistence: reciprocal adaptation promotes the assembly of a simple community

description: Species coexistence may result by chance when co-occurring species do not
 strongly interact or it may be an evolutionary outcome of strongly
 interacting species adapting to each other. While patterns like character
 displacement indicate that coexistence has often been an evolutionary
 outcome, it is unclear how often the evolution of coexistence represents
 adaptation in only one species or reciprocal adaptation among all
 interacting species. Here we demonstrate a strong role for evolution in
 the coexistence of guppies and killifish in Trinidadian streams. We
 experimentally recreated the temporal stages in the invasion and
 establishment of guppies into communities that previously contained only
 killifish. We combined demographic responses of guppies and killifish with
 a size-based integral projection model to calculate the fitness of the
 phenotypes of each species in each of the stages of community assembly. We
 show that guppies from locally adapted populations that are sympatric with
 killifish have higher fitness when paired with killifish than guppies from
 allopatric populations. This elevated fitness involves effects traceable
 to both guppy and killifish evolution. We discuss the implications of our
 results to the study of species coexistence and how it may be mediated
 through eco-evolutionary feedbacks.
description: Guppy Data for
 DryadGuppy demographic
 data
DOI: 10.5061/dryad.0q9g6
title: Data from: A nonrandom subset of olfactory genes is associated with host preference in the fruit fly Drosophila orena

description: Specialization onto different host plants has been hypothesized to be a
 major driver of diversification in insects, and traits controlling
 olfaction have been shown to play a fundamental role in host preferences.
 A diverse set of olfactory genes control olfactory traits in insects, and
 it remains unclear whether specialization onto different hosts is likely
 to involve a nonrandom subset of these genes. Here, we test the role of
 olfactory genes in a novel case of specialization in Drosophila orena. We
 report the first population-level sample of D. orena on the West African
 island of Bioko, since its initial collection in Cameroon in 1975, and use
 field experiments and behavioral assays to show that D. orena has evolved
 a strong preference for waterberry (Syzygium staudtii). We then show that
 a nonrandom subset of genes controlling olfaction-–those controlling
 odorant-binding and chemosensory proteins–-have an enriched signature of
 positive selection relative to the rest of the D. orena genome. By
 comparing signatures of positive selection on olfactory genes between D.
 orena and its sister species, D. erecta we show that odorant-binding and
 chemosensory have evidence of positive selection in both species; however,
 overlap in the specific genes with evidence of selection in these two
 classes is not greater than expected by chance. Finally, we use
 quantitative complementation tests to confirm a role for seven olfactory
 loci in D. orena’s preference for waterberry fruit. Together, our results
 suggest that D. orena and D. erecta have specialized onto different host
 plants through convergent evolution at the level of olfactory gene family,
 but not at specific olfactory genes.
description: eclosion_ratesFile name: eclosion_rates.csv; columns describe: 1-the replicate number; 2-the type of fruit collected; 3:7-the number of individuals of a given species eclosing from that bottle / fruit.field_collectionsFile name: field_collections.txt; columns describe: 1-the altitude of a trapping station; 2-the replicate number at that trapping station; 3-a unique trap identifier; 4-the fruit a trap was bated with ("berries" == waterberry fruit); 5:9-the number of individuals of a given species collected from that trap.food_choice_experimentFile name: food_choice_experiment.csv; columns describe: 1-sex of the flies used in a trial; 2-replicate number for a given combination of sex and species; 3-number of flies that moved into the vial containing the "fruit medley"; 4-number of flies that moved into the vial containing waterberry fruit; 5-the species used in the replicate.performanceFile name: performance.csv; columns describe: 1-species being tested; 2-the substrate they were placed on; 3-the number of progeny eclosing from the vial; 4-a factor name describing the species-substrate combination represented by the replicate.