cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q50h33
title: Data from: The challenges that spatial context present for synthesizing community ecology across scales

description: Accurately characterizing spatial patterns on landscapes is necessary to
 understand the processes that generate biodiversity, a problem that has
 applications in ecological theory, conservation planning, ecosystem
 restoration, and ecosystem management. However, the measurement of
 biodiversity patterns and the ecological and evolutionary processes that
 underlie those patterns is highly dependent on the study unit size,
 boundary placement, and number of observations. These issues, together
 known as the modifiable areal unit problem, are well known in geography.
 These factors limit the degree to which results from different
 metacommunity and macro-ecological studies can be compared to draw new
 inferences, and yet these types of comparisons are widespread in community
 ecology. Using aquatic community datasets, we demonstrate that spatial
 context drives analytical results when landscapes are sub-divided. Next,
 we present a framework for using resampling and neighborhood smoothing to
 standardize datasets to allow for inferential comparisons. We then provide
 examples for how addressing these issues enhances our ability to
 understand the processes shaping ecological communities at landscape
 scales and allows for informative meta-analytical synthesis. We conclude
 by calling for greater recognition of issues derived from the modifiable
 areal unit problem in community ecology, discuss implications of the
 problem for interpreting the existing literature, and identify tools and
 approaches for future research.
description: Maryland
 FishFish communities sampled
 in Maryland between 2007 and 2013. Data were collected by the Maryland
 Biological Stream Survey as part of their regular biomonitoring program.
 Each row contains a unique identifier (SITEYR), the 8 digit watershed code
 (MDE8Digit), the sampling year (Year), the stream name (StreamName),
 spatial coordinates, the 6 digit watershed code (MDE8Digit), the county
 abbreviation (COUNTY), the Fish Index of Biotic Integrity Strata (FIBI),
 and columns for fish abundance.Oikos.MBSS.Fish.csv
DOI: 10.5061/dryad.6n66t
title: Data from: Effects of land use and climate on the distribution of the Jungle Nightjar Caprimulgus indicus in Hokkaido, northern Japan

description: Although the relative importance of land use and climate to large-scale
 bird distributions has received great attention, it is difficult to
 separate the effects of land use and climate, and there are few studies on
 bird abundance distributions on a large scale. Here, we examined the
 effects of land use and climate on the abundance of the nocturnal Jungle
 Nightjar Caprimulgus indicus in Hokkaido, northern Japan. We chose 125
 sampling sites with low correlations (|r| &lt; 0.58) between land use
 and climate, and combined a playback method with a hierarchical model
 (N-mixture model). We thereby accounted for the possibility that we could
 not detect all individuals during the field survey. Results show that
 Jungle Nightjar abundance was greater at sites within a 4-km radius of
 moderate forest cover (~75%) and with high average temperatures during the
 breeding season. Moreover, the effects of land-use were greater than those
 of climate. Mapping predictions of Jungle Nightjar abundance indicated
 that suitable areas are distributed in southern and central Hokkaido and
 around the margins of montane zones. Factoring in the covariation of land
 use and climate, land use may be the most important driver of the
 distribution of the Jungle Nightjar in Hokkaido.
description: AppendicesAppendix 1. Maximum, median, and minimum of environmental factors at each sampling site. Appendix 2. Value of each environmental factor at the centre of each 500 × 500-m grid. Appendix 3. Correlation coefficients and scatter plots among five environmental factors at the sampling sites, and histograms of each environmental factor. Appendix 4. Monthly average temperature during the breeding season at each sampling site. Appendix 5. Details of the N-mixture model. Appendix 6. Results of model averaging for the N-mixture models when we used observation clock time and its squared term as explanatory variables in the detection model. Appendix 7. Results of model selection. Appendix 8. Results of the Generalised Linear Mixed Models (GLMMs) used to test for the effect of spatial autocorrelation among sites.
DOI: 10.5061/dryad.9tq97
title: Data from: Predicting the maximum earthquake magnitude from seismic data in Israel and its neighboring countries

description: This paper explores several data mining and time series analysis methods
 for predicting the magnitude of the largest seismic event in the next year
 based on the previously recorded seismic events in the same region. The
 methods are evaluated on a catalog of 9,042 earthquake events, which took
 place between 01/01/1983 and 31/12/2010 in the area of Israel and its
 neighboring countries. The data was obtained from the Geophysical
 Institute of Israel. Each earthquake record in the catalog is associated
 with one of 33 seismic regions. The data was cleaned by removing
 foreshocks and aftershocks. In our study, we have focused on ten most
 active regions, which account for more than 80% of the total number of
 earthquakes in the area. The goal is to predict whether the maximum
 earthquake magnitude in the following year will exceed the median of
 maximum yearly magnitudes in the same region. Since the analyzed catalog
 includes only 28 years of complete data, the last five annual records of
 each region (referring to the years 2006–2010) are kept for testing while
 using the previous annual records for training. The predictive features
 are based on the Gutenberg-Richter Ratio as well as on some new seismic
 indicators based on the moving averages of the number of earthquakes in
 each area. The new predictive features prove to be much more useful than
 the indicators traditionally used in the earthquake prediction literature.
 The most accurate result (AUC = 0.698) is reached by the Multi-Objective
 Info-Fuzzy Network (M-IFN) algorithm, which takes into account the
 association between two target variables: the number of earthquakes and
 the maximum earthquake magnitude during the same year.
description: Preprocessed yearly
 records of seismic eventsTraining data file:
 Top10-all-win2-train.csv (136 records related to years 1988-2005). Testing
 data file: Top10-all-win2-test.csv (49 records related to years
 2006-2010). The data includes only top 10 areas having the highest number
 of earthquakes. The list of top 10 areas is shown in Table 1 of the paper.
 The format of all files in the folder is compatible with the IN / M-IFN
 software.Top10-IFN -
 Upload.zipInformation Network (IN)
 and Multi-Objective Info-Fuzzy Network (M-IFN) SoftwareIN and M-IFN Software
 (V. 1.90 .NET Framework 2.0). Developed by Mark Last. Further information
 is available in the ReadMe file.IFN-22-Oct-2014.zip
DOI: 10.5061/dryad.3n2d5
title: Data from: No apparent cost of evolved immune response in Drosophila melanogaster

description: Maintenance and deployment of the immune system are costly and are hence
 predicted to trade-off with other resource demanding traits, such as
 reproduction. We subjected this long standing idea to test using
 laboratory experimental evolution approach. In the present study,
 replicate populations of Drosophila melanogaster were subjected to three
 selection regimes – I (Infection with Pseudomonas entomophila), S
 (Sham-infection with MgSO4) and U (Unhandled Control). After 30
 generations of selection flies from the I-regime had evolved better
 survivorship upon infection with P. entomophila compared to flies from U
 and S regimes. However, contrary to expectations and previous reports, we
 did not find any evidence of trade-offs between immunity and other
 life-history related traits, such as longevity, fecundity, egg
 hatchability or development time. After 45 generations of selection, the
 selection was relaxed for a set of populations. Even after 15 generations,
 the post-infection survivorship of populations under relaxed selection
 regime did not decline. We speculate that either there is a negligible
 cost to the evolved immune response or that trade-offs occur on traits
 like reproductive behaviour or other immune mechanisms that we have not
 investigated in this study. Our research suggests that at least under
 certain conditions, life-history trade-offs might play little role in
 maintaining variation in immunity.
description: Figure
 1Figure
 S1Figure
 S2
DOI: 10.5061/dryad.p3p0621d
title: Data from: Are gastropods, rather than ants, important dispersers of seeds of myrmecochorous forest herbs?

description: Seed dispersal by ants (myrmecochory) is widespread and seed adaptations
 to myrmecochory are common, especially in the form of fatty appendices
 (elaiosomes). In a recent study, slugs were identified as seed dispersers
 of myrmecochores in a Central European beech forest. Here we used 105
 beech forest sites to test whether myrmecochore presence and abundance is
 related to ant or to gastropod abundance and whether experimentally
 exposed seeds are removed by gastropods. Myrmecochorous plant cover was
 positively related to gastropod abundance, but negatively to ant
 abundance. Gastropods were responsible for most seed removal and elaiosome
 damage, while insects (and rodents) played minor roles. These gastropod
 effects on seeds were independent of region or forest management. We
 suggest that terrestrial gastropods can generally act as seed dispersers
 of myrmecochorous plants or even substitute myrmecochory, especially where
 ants are absent or uncommon.
description: Myrmecochores_ants_gastropods_beech_forestSeed_removal_beech_forestVideo_recordings_arthropods_fieldVideo_recordings_ants_lab
DOI: 10.5061/dryad.5kq4r
title: Data from: An environmental DNA-based method for monitoring spawning activity: a case study, using the endangered Macquarie perch (Macquaria australasica)

description: Determining the timing and location of reproductive events is critical for
 efficient management of species. However, methods currently used for
 aquatic species are costly, time intensive, biased and often require
 destructive or injurious sampling. Hence, developing a non-invasive
 sampling method to accurately determine the timing and location of
 reproduction for aquatic species would be extremely valuable. We conducted
 an experimental and field study to determine the influence of spawning,
 and the mass release of spermatozoa in particular, on environmental DNA
 (eDNA) concentrations. Using a quantitative PCR approach we monitored
 changes in nuclear and mitochondrial eDNA concentrations over time. The
 data from the experimental study and the field survey supported our
 hypothesis that spawning events are characterized by higher concentrations
 of nuclear relative to mitochondrial eDNA. Outside of the reproductive
 period, we find that nuclear and mitochondrial DNA fragments are equally
 abundant in environmental water samples. We have shown that changes in the
 relative abundance of nuclear and mitochondrial eDNA can be used to
 monitor spawning activity of the endangered Macquarie perch. Our method is
 likely to be transferrable to other aquatic species and can be
 particularly useful to increase our understanding of the spawning biology
 of cryptic, rare or threatened species as well as design and evaluate
 environmental management actions and determine species establishment.
description: Macquaria_australasica_experimentalContains the data of the quantitative PCR analyses of all the samples from the experimental study.Macquaria_australasica_experimental_ratiosContains the data of the calculated ratios between nuclear and mitochondrial environmental DNA concentrations for the experimental study.Macquaria_australasica_field_ratiosContains the data of the calculated ratios between nuclear and mitochondrial environmental DNA concentrations for the field study.Rscript_Bylemans et al (MEE)This is the R script which when run on "Macquaria_australasica_experimental.csv", "Macquaria_australasica_ratios.csv" and "Macquaria_australasica_field_ratios.csv" will produce and print Figure 3, 4 and 5 contained within the main manuscript.ReadMeThis readme file describes the data files accompanying the publication "An environmental DNA (eDNA) based method for monitoring spawning activity: a case study using the endangered Macquarie perch (Macquaria australasica)" by Bylemans et al. For any further queries please contact Jonas.Bylemans@canberra.edu.au
DOI: 10.5061/dryad.dt910
title: Data from: The roles of demography and genetics in the early stages of colonization

description: Colonization success increases with the size of the founding group. Both
 demographic and genetic factors underlie this relationship, yet because
 genetic diversity normally increases with numbers of individuals, their
 relative importance remains unclear. Furthermore, their influence may
 depend on the environment and may change as colonization progresses from
 establishment through population growth and then dispersal. We tested the
 roles of genetics, demography and environment in the founding of Tribolium
 castaneum populations. Using three genetic backgrounds (inbred to
 outbred), we released individuals of four founding sizes (2–32) into two
 environments (natal and novel), and measured establishment success,
 initial population growth and dispersal. Establishment increased with
 founding size, whereas population growth was shaped by founding size,
 genetic background and environment. Population growth was depressed by
 inbreeding at small founding sizes, but growth rates were similar across
 genetic backgrounds at large founding size, an interaction indicating that
 the magnitude of the genetic effects depends upon founding population
 size. Dispersal rates increased with genetic diversity. These results
 suggest that numbers of individuals may drive initial establishment, but
 that subsequent population growth and spread, even in the first generation
 of colonization, can be driven by genetic processes, including both
 reduced growth owing to inbreeding depression, and increased dispersal
 with increased genetic diversity.
description: Szucs et al
 2014_Data_for_DryadThe three sheets in the
 file contain all the data used to assess establishment success, population
 growth, and dispersal rates of the populations described in the methods
 section of the manuscript.
DOI: 10.5061/dryad.kd1nm
title: Data from: Evolution of mating behaviour between two populations adapting to common environmental conditions

description: Populations from the same species may be differentiated across contrasting
 environments, potentially affecting reproductive isolation among them.
 When such populations meet in a novel common environment, this isolation
 may be modified by biotic or abiotic factors. Curiously, the latter have
 been overlooked. We filled this gap by performing experimental evolution
 of three replicates of two populations of Drosophila subobscura adapting
 to a common laboratorial environment, and simulated encounters at three
 time points during this process. Previous studies showed that these
 populations were highly differentiated for several life-history traits and
 chromosomal inversions. First, we show initial differentiation for some
 mating traits, such as assortative mating and male mating rate, but not
 others (e.g., female mating latency). Mating frequency increased during
 experimental evolution in both sets of populations. The assortative mating
 found in one population remained constant throughout the adaptation
 process, while disassortative mating of the other population diminished
 across generations. Additionally, differences in male mating rate were
 sustained across generations. This study shows that mating behavior
 evolves rapidly in response to adaptation to a common abiotic environment,
 although with a complex pattern that does not correspond to the quick
 convergence seen for life-history traits.
description: Mating behaviour Data
 Bases of Drosophila subobscuraThis xls file contains
 the original data sets of no-choice and female-choice experiments each in
 a different tab. The no-choice experiments tab is organized in columns and
 as follows. Generation stands for the number of generations the population
 has been in the lab since foundation. Block represents the population
 replica from the respective foundation. Series and Tube stand for the
 assay series number and the tube number of that series, respectively.
 Female and Male are the source populations for the female and the male in
 the cross, respectively; and there are two categories Ad and Gro which
 stand for Adraga and Groningen respectively. The five following parameters
 were measured in seconds: Courtship Latency (elapsed time to the beginning
 of courtship), Courtship Duration (time spent courting), Beginning of the
 Copula (elapsed time to the beginning of copulation), End of the Copula
 (elapsed time to the end of copulation) and Duration of the Copula (time
 spent copulating). The final column is Mating Occurrence, with 0 standing
 for no mating has occurred and 1 for mating has occurred. The
 female-choice experiments tab is organized in a similar way but each
 female has two entries corresponding to her interaction with the two
 different males. Additionally, this data set has three more columns
 corresponding to Female Size, Male Size and Male Colour. Missing values
 are represented by MV.data_sets_mating_behaviour_dsubobscura_Barbaro_2015.xlsx
DOI: 10.5061/dryad.f3d2m
title: Data from: Genotype and diet shape resistance and tolerance across distinct phases of bacterial infection

description: Background: Host defense against pathogenic infection is composed of
 resistance and tolerance. Resistance is the ability of the host to limit a
 pathogen burden, whereas tolerance is the ability to limit the deleterious
 effects of a given pathogen burden. This distinction recognizes that the
 fittest host does not necessarily have the most aggressive immune system,
 suggesting that host-pathogen co-evolution involves more than an
 escalating arms race between pathogen virulence factors and host
 antimicrobial activity. How a host balances resistance and tolerance and
 how this balance influences the evolution of host defense remains
 unanswered. In order to determine how genotype-by-diet interactions and
 evolutionary costs of each strategy may constrain the evolution of host
 defense, we measured survival, fecundity, and pathogen burden over five
 days in ten genotypes of Drosophila melanogaster reared on two diets and
 infected with the Gram-negative bacterial pathogen Providencia rettgeri.
 Results: We demonstrated two distinct phases of infection: an acute phase
 that consists of high mortality, low fecundity, and high pathogen loads,
 and a chronic phase where there was a substantial but stable pathogen load
 and mortality and fecundity returned to uninfected levels. We demonstrated
 genetic variation for resistance in both phases of infection, but found
 genetic variation for tolerance only in the acute phase. We found
 genotype-by-diet interactions for tolerance, especially in the acute
 phase, but genotype-by-diet interaction did not significantly shape
 resistance. We found a diet-dependent positive relationship between
 resistance and tolerance and a weak evolutionary cost of resistance, but
 did not detect any costs of tolerance. Conclusions: Existing models of
 tolerance and resistance are overly simplistic. Multi-phase infections
 such as that studied here are rarely considered, but we show important
 differences in determination and evolutionary constraints on tolerance and
 resistance over the two phases of infection. Our observation of genetic
 variation for tolerance is inconsistent with simple models that predict
 evolutionary fixation of tolerance alleles, and instead indicate that
 genetic variation for resistance and tolerance is likely to be maintained
 by non-independence between resistance and tolerance, condition-dependent
 evolutionary costs, and environmental heterogeneity.
description: Fecundity Tolerance
 DataHowickfectoldataprepfordryad.txtBacterial Load Datahowickplatedatafordryad.txtMortality Tolerance DataMortTolDataforDryad.txt
DOI: 10.5061/dryad.pn73j
title: Data from: Phylogeography of the dark fruit-eating bat Artibeus obscurus in the Brazilian Amazon

description: Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America,
 being found in at least 18 Brazilian states. Recent studies revealed that
 different populations of this genus present distinct phylogeographic
 patterns; however, very little is known on the population genetics
 structure of A. obscurus in the Amazon rainforest. Here, using a fragment
 (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we
 investigated patterns of genetic divergence among populations of A.
 obscurus from different locations in the Brazilian Amazon rainforest and
 compared them with other Brazilian and South American regions. Analysis of
 molecular variance (AMOVA), fixation index (Fst) analysis, and
 phylogeographic patterns showed divergence between two major monophyletic
 groups, each one corresponding to a geographic region associated with the
 Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a
 monophyletic group with a high bootstrap support and a fragmented
 distribution that follows the pattern predicted by the Refuge Theory. On
 the other hand, a different scenario was observed for the Amazon forest,
 where no fragmentation was identified. The AMOVA results revealed a
 significant geographic heterogeneity in the distribution of genetic
 variation, with 70% found within populations across the studied
 populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The
 intrapopulational analysis revealed that one population (Bragança) showed
 significant evidence of population expansion, with the formation of 2
 distinct phylogroups, suggesting the occurrence of a subspecies or at
 least a different population in this region. These results also suggest
 considerable heterogeneity for A. obscurus in the Amazon region.
description: NetworkHaplotype networknetwork.gml
DOI: 10.5061/dryad.2q6p8
title: Data from: On the relationship between ontogenetic and static allometry

description: Ontogenetic and static allometries describe how a character changes in
 size when the size of the organism changes during ontogeny and among
 individuals measured at the same developmental stage, respectively.
 Understanding the relationship between these two types of allometry is
 crucial to understanding the evolution of allometry and, more generally,
 the evolution of shape. However, the effects of ontogenetic allometry on
 static allometry remain largely unexplored. Here, we first show
 analytically how individual variation in ontogenetic allometry and body
 size affect static allometry. Using two longitudinal data sets on
 ontogenetic and static allometry, we then estimate variances and
 covariances for the different parameters of the ontogenetic allometry
 defined in our model and assess their relative contribution to the static
 allometric slope. The mean ontogenetic allometry is the main parameter
 that determines the static allometric slope, while the covariance between
 the ontogenetic allometric slope and body size generates most of the
 discrepancies between ontogenetic and static allometry. These results
 suggest that the apparent evolutionary stasis of the static allometric
 slope is not generated by internal (developmental) constraints but more
 likely results from external constraints imposed by selection.
description: Pelabon et al Guppy
 datameasurements collected
 by C.K. Egset on guppy maintained in captivity.Pelabon et al Mouse
 LongitudinalMeasurements collected
 by J. Cheverud.