cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3rh21
title: Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

description: 1. The biodiversity of mixed-species samples of arthropods can be
 characterized by shotgun sequencing of bulk genomic DNA and subsequent
 bioinformatics assembly of mitochondrial genomes. Here, we tested the
 power of mitochondrial metagenomics by conducting Illumina sequencing on
 mixtures of &gt;2600 individuals of leaf beetles (Chrysomelidae) from
 10 communities. 2. Patterns of species richness, community dissimilarity
 and biomass were assessed from matches of reads against three reference
 databases, including (i) a custom set of mitogenomes generated for 156
 species (89% of species in the study); (ii) mitogenomes obtained by the de
 novo assembly of sequence reads from the real-world communities; and (iii)
 a custom set of DNA barcode (cox1-5′) sequences. 3. Species detection
 against the custom-built reference genomes was very high (&gt;90%).
 False presences were rare against mitogenomes but slightly higher against
 the barcode references. False absences were mainly due to the
 incompleteness of the reference databases and, thus, more prevalent in the
 de novo data set. Biomass (abundance × body length) and read numbers were
 strongly correlated, demonstrating the potential of mitochondrial
 metagenomics for studies of species abundance. 4. A phylogenetic tree from
 the mitogenomes showed high congruence with known relationships in
 Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity
 between sites were highly consistent with data from morphological
 identifications. 5. The power of mitochondrial metagenomics results from
 the possibility of rapid assembly of mitogenomes from mixtures of
 specimens and the use of read counts for accurate estimates of key
 parameters of biodiversity directly from community samples.
description: Mitochondrial genomes
 (complete or partialI) of leaf beetles in the MitoRL and
 DeNovoRLContigs produced by
 shotgun sequencing of bulk genomic DNA (Illumina) and subsequent
 bioinformatics assembly. Contigs belong to two different reference
 libraries: a custom-built “mitochondrial reference library” (“MitoRL”) and
 a database of mitogenomes obtained by the de novo assembly of sequence
 reads from 10 real-world assemblages of leaf beetles
 ("DeNovoRL"). In the DeNovoRL, contigs were assembled
 individually for each sampling locality (“LocL”, the sampling locality is
 specified ) or combined for all ten libraries (“CombL”). An acronynm of
 species name is shown for each contig.Gomez-Rodriguez et
 al.fasta
DOI: 10.5061/dryad.33ps4
title: Data from: Geographies of an online social network

description: How is online social media activity structured in the geographical space?
 Recent studies have shown that in spite of earlier visions about the
 “death of distance”, physical proximity is still a major factor in social
 tie formation and maintenance in virtual social networks. Yet, it is
 unclear, what are the characteristics of the distance dependence in online
 social networks. In order to explore this issue the complete network of
 the former major Hungarian online social network is analyzed. We find that
 the distance dependence is weaker for the online social network ties than
 what was found earlier for phone communication networks. For a further
 analysis we introduced a coarser granularity: We identified the
 settlements with the nodes of a network and assigned two kinds of weights
 to the links between them. When the weights are proportional to the number
 of contacts we observed weakly formed, but spatially based modules
 resemble to the borders of macro-regions, the highest level of regional
 administration in the country. If the weights are defined relative to an
 uncorrelated null model, the next level of administrative regions,
 counties are reflected.
description: iWiW_town_networkThe data is stored in two csv files. 1. iWiW_town_nodes.csv includes characteristics of 2558 towns. The file is structured into 7 coloumns as follows: “id” – key to match node characteristics into edgelist. “town” – name of towns. “user” – number of registered iWiW users in the town. “pop” – number of inhabitants in the town. “latitude” – geo-coordinates (latitude) of the town. “longitude” – geo-coordinates (longitude) of the town. “code” – unique identifier of the town in databases of the Hungarian Statistical Office. This key can be used to match the data with further town characteristics. 2. iWiW_town_edges.csv includes “id1” – identifier of town i, which can be used as a key to match node characteristics into edgelist. “id2” – identifier of town j, which can be used as a key to match node characteristics into edgelist. “connect” – the number of friendship ties between towns i and j.
DOI: 10.5061/dryad.6m761
title: Data from: Fitness costs in spatially structured environments

description: The clustering of individuals that results from limited dispersal is a
 double-edged sword: while it allows for local interactions to be mostly
 among related individuals, it also results in increased local competition.
 Here I show that, because they mitigate local competition, fitness costs
 such as reduced fecundity or reduced survival are less costly in spatially
 structured environments than in non spatial settings. I first present a
 simple demographic example to illustrate how spatial structure weakens
 selection against fitness costs. Then, I illustrate the importance of
 disentangling the evolution of a trait from the evolution of potential
 associated costs, using an example taken from a recent study investigating
 the effect of spatial structure on the evolution of host defense. In this
 example indeed, the differences between spatial and non-spatial selection
 gradients are due to differences in the fitness costs, thereby undermining
 interpretations of the results made in terms of the trait only. This
 illustrates the need to consider fitness costs as proper traits in both
 theoretical and empirical studies.
description: Debarre_2015_EvolutionZipped folder containing the scripts to re-run and plot all the figures presented in the article.
DOI: 10.5061/dryad.sk55m
title: Data from: Do humans optimally exploit redundancy to control step variability in walking?

description: It is widely accepted that humans and animals minimize energetic cost
 while walking. While such principles predict average behavior, they do not
 explain the variability observed in walking. For robust performance,
 walking movements must adapt at each step, not just on average. Here, we
 propose an analytical framework that reconciles issues of optimality,
 redundancy, and stochasticity. For human treadmill walking, we defined a
 goal function to formulate a precise mathematical definition of one
 possible control strategy: maintain constant speed at each stride. We
 recorded stride times and stride lengths from healthy subjects walking at
 five speeds. The specified goal function yielded a decomposition of
 stride-to-stride variations into new gait variables explicitly related to
 achieving the hypothesized strategy. Subjects exhibited greatly decreased
 variability for goal-relevant gait fluctuations directly related to
 achieving this strategy, but far greater variability for goal-irrelevant
 fluctuations. More importantly, humans immediately corrected goal-relevant
 deviations at each successive stride, while allowing goal-irrelevant
 deviations to persist across multiple strides. To demonstrate that this
 was not the only strategy people could have used to successfully
 accomplish the task, we created three surrogate data sets. Each tested a
 specific alternative hypothesis that subjects used a different strategy
 that made no reference to the hypothesized goal function. Humans did not
 adopt any of these viable alternative strategies. Finally, we developed a
 sequence of stochastic control models of stride-to-stride variability for
 walking, based on the Minimum Intervention Principle. We demonstrate that
 healthy humans are not precisely “optimal,” but instead consistently
 slightly over-correct small deviations in walking speed at each stride.
 Our results reveal a new governing principle for regulating
 stride-to-stride fluctuations in human walking that acts independently of,
 but in parallel with, minimizing energetic cost. Thus, humans exploit task
 redundancies to achieve robust control while minimizing effort and
 allowing potentially beneficial motor variability.
description: Young_Healthy_Mat_FilesYoung Healthy (YH) Subjects -- Data in Matlab Mat-File FormatOlder_Healthy_Mat_FilesOlder Healthy (OH) Subjects -- Data in Matlab Mat-File FormatYoung_Healthy_CSV_FilesYoung Healthy (YH) Subjects -- Data in CSV-File FormatOlder_Healthy_CSV_FilesOlder Healthy (OH) Subjects -- Data in CSV-File Format
DOI: 10.5061/dryad.kv028
title: Data from: Models of knot and stem development in black spruce trees indicate a shift in allocation priority to branches when growth is limited

description: The branch autonomy principle, which states that the growth of individual
 branches can be predicted from their morphology and position in the forest
 canopy irrespective of the characteristics of the tree, has been used to
 simplify models of branch growth in trees. However, observed changes in
 allocation priority within trees towards branches growing in
 light-favoured conditions, referred to as ‘Milton’s Law of resource
 availability and allocation,’ have raised questions about the
 applicability of the branch autonomy principle. We present models linking
 knot ontogeny to the secondary growth of the main stem in black spruce
 (Picea mariana (Mill.) B.S.P.), which were used to assess the patterns of
 assimilate allocation over time, both within and between trees. Data
 describing the annual radial growth of 445 stem rings and the
 three-dimensional shape of 5,377 knots were extracted from optical scans
 and X-ray computed tomography images taken along the stems of 10 trees.
 Total knot to stem area increment ratios (KSR) were calculated for each
 year of growth, and statistical models were developed to describe the
 annual development of knot diameter and curvature as a function of stem
 radial increment, total tree height, stem diameter, and the position of
 knots along an annual growth unit. KSR varied as a function of tree age
 and of the height to diameter ratio of the stem, a variable indicative of
 the competitive status of the tree. Simulations of the development of an
 individual knot showed that an increase in the stem radial growth rate was
 associated with an increase in the initial growth of the knot, but also
 with a shorter lifespan. Our results provide support for ‘Milton’s Law,’
 since they indicate that allocation priority is given to locations where
 the potential return is the highest. The developed models provided
 realistic simulations of knot morphology within trees, which could be
 integrated into a functional-structural model of tree growth and
 above-ground resource partitioning.
description: Tree Rings and knots
 measurementsTree, Ring and knot data
 used in the article 10.7717/peerj.873.Data_publish.xlsx
DOI: 10.5061/dryad.5h032
title: Data from: Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion

description: Organisms exhibit an incredible diversity of life history strategies as
 adaptive responses to environmental variation. The establishment of novel
 life history strategies involves multilocus polymorphisms, which will be
 challenging to establish in the face of gene flow and recombination.
 Theory predicts that adaptive allelic combinations may be maintained and
 spread if they occur in genomic regions of reduced recombination, such as
 chromosomal inversion polymorphisms, yet empirical support for this
 prediction is lacking. Here, we use genomic data to investigate the
 evolution of divergent adaptive ecotypes of the yellow monkey flower
 Mimulus guttatus. We show that a large chromosomal inversion polymorphism
 is the major region of divergence between geographically widespread annual
 and perennial ecotypes. In contrast, ∼40,000 single nucleotide
 polymorphisms in collinear regions of the genome show no signal of life
 history, revealing genomic patterns of diversity have been shaped by
 localized homogenizing gene flow and large-scale Pleistocene range
 expansion. Our results provide evidence for an inversion capturing and
 protecting loci involved in local adaptation, while also explaining how
 adaptive divergence can occur with gene flow.
description: Twyford Mimulus guttatus
 aligned GBS SNPs for North American phylogeographyVCF file of
 reference-sequence aligned SNPs from a genotyping by sequencing
 experiment. Individual Mimulus samples were collected in the field, and
 SNP calls were made with the TASSEL-GBS pipeline.Twyford_Mimulus_guttatus_all_aligned_GBS_SNPs.vcfBayesian phylogenetic tree for North American samples of Mimulus guttatus
DOI: 10.5061/dryad.h9083
title: Data from: Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

description: 1. Plant functional traits, in particular specific leaf area (SLA), wood
 density and seed mass, are often good predictors of individual tree growth
 rates within communities. Individuals and species with high SLA, low wood
 density and small seeds tend to have faster growth rates. 2. If
 community-level relationships between traits and growth have general
 predictive value, then similar relationships should also be observed in
 analyses that integrate across taxa, biogeographic regions and
 environments. Such global consistency would imply that traits could serve
 as valuable proxies for the complex suite of factors that determine growth
 rate, and, therefore, could underpin a new generation of robust dynamic
 vegetation models. Alternatively, growth rates may depend more strongly on
 the local environment or growth–trait relationships may vary along
 environmental gradients. 3. We tested these alternative hypotheses using
 data on 27 352 juvenile trees, representing 278 species from 27 sites on
 all forested continents, and extensive functional trait data, 38% of which
 were obtained at the same sites at which growth was assessed. Data on
 potential evapotranspiration (PET), which summarizes the joint ecological
 effects of temperature and precipitation, were obtained from a global data
 base. 4. We estimated size-standardized relative height growth rates (SGR)
 for all species, then related them to functional traits and PET using
 mixed-effect models for the fastest growing species and for all species
 together. 5. Both the mean and 95th percentile SGR were more strongly
 associated with functional traits than with PET. PET was unrelated to SGR
 at the global scale. SGR increased with increasing SLA and decreased with
 increasing wood density and seed mass, but these traits explained only
 3.1% of the variation in SGR. SGR–trait relationships were consistently
 weak across families and biogeographic zones, and over a range of tree
 statures. Thus, the most widely studied functional traits in plant ecology
 were poor predictors of tree growth over large scales. 6. Synthesis. We
 conclude that these functional traits alone may be unsuitable for
 predicting growth of trees over broad scales. Determining the functional
 traits that predict vital rates under specific environmental conditions
 may generate more insight than a monolithic global relationship can offer.
description: Growth and functional
 trait data for 287 tree speciesSee read-me
 fileData
 for Dryad - Paine et al 2015 Journal of
 Ecology.zip
DOI: 10.5061/dryad.8297
title: Data from: High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries

description: Microsatellites (or SSR: simple sequence repeat) are among the most
 frequently used DNA markers in many areas of research. The use of
 microsatellite markers is limited by the difficulties involved in their de
 novo isolation from species for which no genomic resources are available.
 We describe here a high-throughput method for isolating microsatellite
 markers based on coupling multiplex microsatellite enrichment and
 Next-Generation Sequencing on 454 GS-FLX Titanium platforms. The procedure
 was calibrated on a model species (Apis mellifera) and validated on 13
 other species from various taxonomic groups (animals, plants, fungi),
 including taxa for which severe difficulties were previously encountered
 using traditional methods. We obtained from 11,497 to 34,483 sequences
 depending on the species and the number of detected microsatellite loci
 ranged from 199 to 5,791. We thus demonstrated that this procedure can be
 readily and successfully applied to a large variety of taxonomic groups,
 at much lower cost than would have been possible with traditional
 protocols. This method is expected to speed up the acquisition of
 high-quality genetic markers for nonmodel organisms.
description: Malausa_et_al_MER_Dryad
DOI: 10.5061/dryad.36t0k
title: Data from: Can butterflies evade fire? Pupa location and heat tolerance in fire prone habitats of Florida

description: Butterflies such as the atala hairstreak, Eumaeus atala Poey, and the
 frosted elfin, Callophrys irus Godart, are restricted to frequently
 disturbed habitats where their larval host plants occur. Pupae of these
 butterflies are noted to reside at the base of host plants or in the leaf
 litter and soil, which may allow them to escape direct mortality by fire,
 a prominent disturbance in many areas they inhabit. The capacity of these
 species to cope with fire is a critical consideration for land management
 and conservation strategies in the locations where they are found.
 Survival of E. atala pupae in relation to temperature and duration of heat
 pulse was tested using controlled water bath experiments and a series of
 prescribed fire field experiments. Survival of E. atala pupae was
 correlated to peak temperature and heat exposure in both laboratory and
 field trials. In addition, E. atala survival following field trials was
 correlated to depth of burial; complete mortality was observed for pupae
 at the soil surface. Fifty percent of E. atala survived the heat generated
 by prescribed fire when experimentally placed at depths ≥ 1.75cm,
 suggesting that pupation of butterflies in the soil at depth can protect
 from fatal temperatures caused by fire. For a species such as E. atala
 that pupates above ground, a population reduction from a burn event is a
 significant loss, and so decreasing the impact of prescribed fire on
 populations is critical.
description: iButton temperature
 measurementsThis data file contains
 all of the logged temperatures during the prescribed fire field
 experiments involving buried Eumaeus atala butterfly pupae. The iButton
 temperature sensors were buried in the sandy soil at the described depths
 within the file. This file is a transfer of all the downloaded data from
 up to 25 different iButton sensors used in the prescribed fire field
 experiments.burntemplogs.xlsx7-5-12 burn laser therm measurementsSoil surface temperatures measured with a handheld infrared thermometer during the prescribed burn experiments.7-6-12 burn laser therm measurementsSoil surface temperatures measured with a handheld infrared thermometer during the prescribed burn experiments.7-26-12 burn laser therm measurementsSoil surface temperatures measured with a handheld infrared thermometer during the prescribed burn experiments.Field experiment dataContains both the prescribed fire data and integration and the Eumaeus atala survival and demographic information. This file was used for regression analysis.bhexperiment3fieldonly.csvHeat tolerance lab experiment dataContains both the lab temperature data and integration and the Eumaeus atala survival and demographic information. This file was used for regression analysis.bhexperiment3labonly.csv
DOI: 10.5061/dryad.5jq6p
title: Data from: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

description: Models of speciation-with-gene-flow have shown that the reduction in
 recombination between alternative chromosome arrangements can facilitate
 the fixation of locally adaptive genes in the face of gene flow and
 contribute to speciation. However, it has proven frustratingly difficult
 to show empirically that inversions have reduced gene flow and arose
 during or shortly after the onset of species divergence rather than
 represent ancestral polymorphisms. Here we present an analysis of whole
 genome data from a pair of cactophilic fruit flies, Drosophila mojavensis
 and D. arizonae, which are reproductively isolated in the wild and differ
 by several large inversions on three chromosomes. We found an increase in
 divergence at rearranged compared to colinear chromosomes. Using the
 density of divergent sites in short sequence blocks we fit a series of
 explicit models of species divergence in which gene flow is restricted to
 an initial period after divergence and may differ between colinear and
 rearranged parts of the genome. These analyses show that D. mojavensis and
 D. arizonae have experienced post-divergence gene flow which ceased around
 270 KY ago and was significantly reduced in chromosomes with fixed
 inversions. Moreover, we show that these inversions most likely originated
 around the time of of species divergence which is compatible with
 theoretical models of speciation with gene flow.
description: Dryad_data_2015The folder contains .txt files of counts of divergent sites between D. arizonae and D. mojavensis in 250 and 500 bp blocks of intergenic sequence. These are the input files (readable with the Mathematica function ReadList[]) for fitting the IIM model using an analytic expression for the likelihood derived by Wilkinson-Herbots (2012). For details see Methods in Lohse et al (2015). Each block is summarized as a nested list {{S_div, S_het}, total length, pos}. The four entries are: S_div: Number of divergent sites S_het: Number of heterozygous sites in both species total length: Total physical length of the block in the Dmoj reference genome including sites that did not pass filtering. pos: Position on the scaffold (mean position of all called sites) Blocks containing heterozygous sites or a physical length &gt; 2x the number of called sites were not used in the analysis.