cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cn252
title: Data from: Efficiency of lift production in flapping and gliding flight of swifts

description: Many flying animals use both flapping and gliding flight as part of their
 routine behaviour. These two kinematic patterns impose conflicting
 requirements on wing design for aerodynamic efficiency and, in the absence
 of extreme morphing, wings cannot be optimised for both flight modes. In
 gliding flight, the wing experiences uniform incident flow and the optimal
 shape is a high aspect ratio wing with an elliptical planform. In flapping
 flight, on the other hand, the wing tip travels faster than the root,
 creating a spanwise velocity gradient. To compensate, the optimal wing
 shape should taper towards the tip (reducing the local chord) and/or twist
 from root to tip (reducing local angle of attack). We hypothesised that,
 if a bird is limited in its ability to morph its wings and adapt its wing
 shape to suit both flight modes, then a preference towards flapping flight
 optimization will be expected since this is the most energetically
 demanding flight mode. We tested this by studying a well-known
 flap-gliding species, the common swift, by measuring the wakes generated
 by two birds, one in gliding and one in flapping flight in a wind tunnel.
 We calculated span efficiency, the efficiency of lift production, and
 found that the flapping swift had consistently higher span efficiency than
 the gliding swift. This supports our hypothesis and suggests that even
 though swifts have been shown previously to increase their lift-to-drag
 ratio substantially when gliding, the wing morphology is tuned to be more
 aerodynamically efficient in generating lift during flapping. Since body
 drag can be assumed to be similar for both flapping and gliding, it
 follows that the higher total drag in flapping flight compared with
 gliding flight is primarily a consequence of an increase in wing profile
 drag due to the flapping motion, exceeding the reduction in induced drag.
description: Vector fields of
 flapping and gliding swiftsFlow measurements behind
 swifts (Apus apus) in flapping and gliding flight in the Lund University
 wind tunnel. The data are in the form of vector fields in DaVis
 VC7-format. The zipped file contains two folders, one holding all the
 sequences from the flapping flight experiments and one all the sequences
 from the gliding flight experiments. Each of these folders contains
 sub-folders with names corresponding to the flight speed examined during
 measurements. Inside these subfolders sequences are located and the names
 of each of them show time and date of acquisition and the major processing
 steps performed in DaVis. Only sections within these sequences
 corresponding to steady flight where the complete semi wake span is
 present were used for analysis.Vector_fields_Swifts.zip
DOI: 10.5061/dryad.bm4f9n0
title: Data from: Accounting for disturbance history in models: using remote sensing to constrain carbon and nitrogen pool spin‐up

description: Disturbances such as wildfire, insect outbreaks, and forest clearing, play
 an important role in regulating carbon, nitrogen, and hydrologic fluxes in
 terrestrial watersheds. Evaluating how watersheds respond to disturbance
 requires understanding mechanisms that interact over multiple spatial and
 temporal scales. Simulation modeling is a powerful tool for bridging these
 scales; however, model projections are limited by uncertainties in the
 initial state of plant carbon and nitrogen stores. Watershed models
 typically use one of two methods to initialize these stores: spin-up to
 steady state, or remote sensing with allometric relationships. Spin-up
 involves running a model until vegetation reaches equilibrium based on
 climate; this approach assumes that vegetation across the watershed has
 reached maturity and is of uniform age, which fails to account for
 landscape heterogeneity and non-steady state conditions. By contrast,
 remote sensing, can provide data for initializing such conditions.
 However, methods for assimilating remote sensing into model simulations
 can also be problematic. They often rely on empirical allometric
 relationships between a single vegetation variable and modeled carbon and
 nitrogen stores. Because allometric relationships are species- and
 region-specific, they do not account for the effects of local resource
 limitation, which can influence carbon allocation (to leaves, stems,
 roots, etc.). To address this problem, we developed a new initialization
 approach using the catchment-scale ecohydrologic model RHESSys. The new
 approach merges the mechanistic stability of spin-up with the spatial
 fidelity of remote sensing. It uses remote sensing to define spatially
 explicit targets for one, or several vegetation state variables, such as
 leaf area index, across a watershed. The model then simulates the growth
 of carbon and nitrogen stores until the defined targets are met for all
 locations. We evaluated this approach in a mixed pine-dominated watershed
 in central Idaho, and a chaparral-dominated watershed in southern
 California. In the pine-dominated watershed, model estimates of carbon,
 nitrogen, and water fluxes varied among methods, while the target-driven
 method increased correspondence between observed and modeled streamflow.
 In the chaparral watershed, where vegetation was more homogeneously aged,
 there were no major differences among methods. Thus, in heterogeneous,
 disturbance-prone watersheds, the target-driven approach shows potential
 for improving biogeochemical projections.
description: Inputs, settings, and
 state variables for RHESSys simulationsThis includes all files
 necessary to run RHESSys simulations with the file structure already set
 up.HananCinitialization.tgz
DOI: 10.5061/dryad.ms8k7
title: Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

description: The evolutionary history of the human pygmy phenotype (small body size), a
 characteristic of African and Southeast Asian rainforest hunter-gatherers,
 is largely unknown. Here we use a genome-wide admixture mapping analysis
 to identify 16 genomic regions that are significantly associated with the
 pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from
 Uganda (east central Africa). The identified genomic regions have multiple
 attributes that provide supporting evidence of genuine association with
 the pygmy phenotype, including enrichments for SNPs previously associated
 with stature variation in Europeans and for genes with growth hormone
 receptor and regulation functions. To test adaptive evolutionary
 hypotheses, we computed the haplotype-based integrated haplotype score
 (iHS) statistic and the level of population differentiation (FST) between
 the Batwa and their agricultural neighbors, the Bakiga, for each genomic
 SNP. Both |iHS| and FST values were significantly higher for SNPs within
 the Batwa pygmy phenotype-associated regions than the remainder of the
 genome, a signature of polygenic adaptation. In contrast, when we expanded
 our analysis to include Baka rainforest hunter-gatherers from Cameroon and
 Gabon (west central Africa) and Nzebi and Nzime neighboring
 agriculturalists, we did not observe elevated |iHS| or FST values in these
 genomic regions. Together, these results suggest adaptive and at least
 partially convergent origins of the pygmy phenotype even within Africa,
 supporting the hypothesis that small body size confers a selective
 advantage for tropical rainforest hunter-gatherers but raising questions
 about the antiquity of this behavior.
description: Supplementary Data for
 Perry et al. PNAS (all files)
DOI: 10.5061/dryad.rm505
title: Data from: Evidence for a time-invariant phase variable in human ankle control

description: Human locomotion is a rhythmic task in which patterns of muscle activity
 are modulated by state-dependent feedback to accommodate perturbations.
 Two popular theories have been proposed for the underlying embodiment of
 phase in the human pattern generator: a time-dependent internal
 representation or a time-invariant feedback representation (i.e., reflex
 mechanisms). In either case the neuromuscular system must update or
 represent the phase of locomotor patterns based on the system state, which
 can include measurements of hundreds of variables. However, a much simpler
 representation of phase has emerged in recent designs for legged robots,
 which control joint patterns as functions of a single monotonic mechanical
 variable, termed a phase variable. We propose that human joint patterns
 may similarly depend on a physical phase variable, specifically the
 heel-to-toe movement of the Center of Pressure under the foot. We found
 that when the ankle is unexpectedly rotated to a position it would have
 encountered later in the step, the Center of Pressure also shifts forward
 to the corresponding later position, and the remaining portion of the gait
 pattern ensues. This phase shift suggests that the progression of the
 stance ankle is controlled by a biomechanical phase variable, motivating
 future investigations of phase variables in human locomotor control.
description: Data from: Evidence for
 a Time-Invariant Phase Variable in Human Ankle ControlReadme file for data
 used in study: "Evidence for a Time-Invariant Phase Variable in Human
 Ankle Control" R D Gregg, E J Rouse, L J Hargrove and J W Sensinger
 PLOS ONE For questions regarding the data, please contact the authors:
 Robert Gregg (rgregg@utdallas.edu) or Elliott Rouse
 (erouse@media.mit.edu)data.zip
DOI: 10.5061/dryad.h9v504t
title: Data from: Rhythmic motor behavior influences perception of visual time

description: Temporal processing is fundamental for an accurate synchronization between
 motor behavior and sensory processing. Here we investigate how motor
 timing during rhythmic tapping influences perception of visual time.
 Participants listen to a sequence of four auditory tones played at 1 Hz
 and continue the sequence (without auditory stimulation) by tapping four
 times with their finger. During finger tapping, they are presented with an
 empty visual interval and are asked to judge its length compared to a
 previously internalized interval of 150 ms. The visual temporal estimates
 show non-monotonic changes locked to the finger tapping: perceived time is
 maximally expanded at half time between the two consecutive finger taps,
 and maximally compressed near tap onsets. Importantly, the temporal
 dynamics of the perceptual time distortion scales linearly with the timing
 of the motor tapping, with maximal expansion being always anchored to the
 center of the inter-tap interval. These results reveal an intrinsic
 coupling between distortion of perceptual time and production of
 self-timed motor rhythms, suggesting the existence of a timing mechanism
 that keeps perception and action accurately synchronized.
description: MainExp_rawdata
DOI: 10.5061/dryad.v2st1
title: Data from: Detection of tephra layers in Antarctic sediment cores with hyperspectral imaging

description: Tephrochronology uses recognizable volcanic ash layers (from airborne
 pyroclastic deposits, or tephras) in geological strata to set unique time
 references for paleoenvironmental events across wide geographic areas.
 This involves the detection of tephra layers which sometimes are not
 evident to the naked eye, including the so-called cryptotephras. Tests
 that are expensive, time-consuming, and/or destructive are often required.
 Destructive testing for tephra layers of cores from difficult regions,
 such as Antarctica, which are useful sources of other kinds of information
 beyond tephras, is always undesirable. Here we propose hyperspectral
 imaging of cores, Self-Organizing Map (SOM) clustering of the preprocessed
 spectral signatures, and spatial analysis of the classified images as a
 convenient, fast, non-destructive method for tephra detection. We test the
 method in five sediment cores from three Antarctic lakes, and show its
 potential for detection of tephras and cryptotephras.
description: Data_IsmaelAymerich_PLOSONE_2015Excel file containing hyperspectral signatures of tephra and No-tephra samples extracted from an Antarctic sediment core. Tephra signatures are labelled 1, while No-tephra spectra are labelled 0.
DOI: 10.5061/dryad.hs2g9
title: Data from: Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics

description: Ancient and archival DNA samples are valuable resources for the study of
 diverse historical processes. In particular, museum specimens provide
 access to biotas distant in time and space, and can provide insights into
 ecological and evolutionary changes over time. However, archival specimens
 are difficult to handle; they are often fragile and irreplaceable, and
 typically contain only short segments of denatured DNA. Here we present a
 set of tools for processing such samples for state-of-the-art genetic
 analysis. First, we report a protocol for minimally destructive DNA
 extraction of insect museum specimens, which produced sequenceable DNA
 from all of the samples assayed. The 11 specimens analyzed had fragmented
 DNA, rarely exceeding 100 bp in length, and could not be amplified by
 conventional PCR targeting the mitochondrial cytochrome oxidase I gene.
 Our approach made these samples amenable to analysis with commonly used
 next-generation sequencing-based molecular analytic tools, including
 RAD-tagging and shotgun genome re-sequencing. First, we used museum ant
 specimens from three species, each with its own reference genome, for
 RAD-tag mapping. Were able to use the degraded DNA sequences, which were
 sequenced in full, to identify duplicate reads and filter them prior to
 base calling. Second, we re-sequenced six Hawaiian Drosophila species,
 with millions of years of divergence, but with only a single available
 reference genome. Despite a shallow coverage of 0.37±0.42 per base, we
 could recover a sufficient number of overlapping SNPs to fully resolve the
 species tree, which was consistent with earlier karyotypic studies, and
 previous molecular studies, at least in the regions of the tree that these
 studies could resolve. Although developed for use with degraded DNA, all
 of these techniques are readily applicable to more recent tissue, and are
 suitable for liquid handling automation.
description: Genomic reads of 6
 Hawaiian Drosophila species mapped to the D. grimshawi
 genomeFile is in standard BAM
 format. Species names are identified by read groups
 IDs.drosophila.bamRAD-tag reads mapped to reference ant genomesThe archive contains 6 BAM files with genomic reads from three species of ants mapped to their respective reference genomes.ants.tar
DOI: 10.5061/dryad.s38n5
title: Data from: Neural modularity helps organisms evolve to learn new skills without forgetting old

description: A long-standing goal in artificial intelligence is creating agents that
 can learn a variety of different skills for different problems. In the
 artificial intelligence subfield of neural networks, a barrier to that
 goal is that when agents learn a new skill they typically do so by losing
 previously acquired skills, a problem called catastrophic forgetting. That
 occurs because, to learn the new task, neural learning algorithms change
 connections that encode previously acquired skills. How networks are
 organized critically affects their learning dynamics. In this paper, we
 test whether catastrophic forgetting can be reduced by evolving modular
 neural networks. Modularity intuitively should reduce learning
 interference between tasks by separating functionality into physically
 distinct modules in which learning can be selectively turned on or off.
 Modularity can further improve learning by having a reinforcement learning
 module separate from sensory processing modules, allowing learning to
 happen only in response to a positive or negative reward. In this paper,
 learning takes place via neuromodulation, which allows agents to
 selectively change the rate of learning for each neural connection based
 on environmental stimuli (e.g. to alter learning in specific locations
 based on the task at hand). To produce modularity, we evolve neural
 networks with a cost for neural connections. We show that this connection
 cost technique causes modularity, confirming a previous result, and that
 such sparsely connected, modular networks have higher overall performance
 because they learn new skills faster while retaining old skills more and
 because they have a separate reinforcement learning module. Our results
 suggest (1) that encouraging modularity in neural networks may help us
 overcome the long-standing barrier of networks that cannot learn new
 skills without forgetting old ones, and (2) that one benefit of the
 modularity ubiquitous in the brains of natural animals might be to
 alleviate the problem of catastrophic forgetting.
description: data_and_plotting_scriptsThe data were generated by experiments in the Sferes evolutionary algorithm framework. Source code for our experiments are available at: http://evolvingai.org/code/modularity_forgetting.tar.gz
DOI: 10.5061/dryad.121d03jc
title: Data from: Chemical element distributions within conodont elements and their functional implications

description: Electron microprobe analyses of platform (pectiniform Pa) elements of
 Permian conodonts reveal detailed and systematic chemical element
 distributions. The crown of the conodont element is more densely
 mineralized than the basal body and shows evidence of less dense
 mineralization in areas of rapid growth. Patterns in sodium and sulfur
 concentrations indicate oral to aboral differentiation within conodont
 elements. These chemical element patterns support oral exposure during
 life and functional use as a tooth, and they approximate the erupted and
 embedded positions of the conodont tooth when the animal was alive.
 Previously unrecognized spatial distributions of geochemically important
 chemical elements warrant consideration in future geochemical studies of
 conodonts.
description: Supplementary Data Read
 Me FileSupplementary
 Table1Supplementary
 Table2Supplementary
 Table3Supplementary
 Table4Supplementary
 Table1csvSupplementary
 Table2csvSupplementary
 Table3csvSupplementary
 Table4csvSupplementary
 Figure1Supplementary
 Figure2
DOI: 10.5061/dryad.n816r
title: Data from: Draft genome of the American eel (Anguilla rostrata)

description: Freshwater eels (Anguilla sp.) have large economic, cultural, ecological
 and aesthetic importance worldwide, but they suffered more than 90%
 decline in global stocks over the past few decades. Proper genetic
 resources, such as sequenced, assembled and annotated genomes, are
 essential to help plan sustainable recoveries by identifying
 physiological, biochemical and genetic mechanisms that caused the declines
 or that may lead to recoveries. Here, we present the first sequenced
 genome of the American Eel. This genome contained 305,043 contigs (N50 =
 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1.41 Gb,
 which is in the middle of the range of previous estimations for this
 species. In addition, protein coding regions, including introns and
 flanking regions, are very well represented in the genome, as 95.2% of the
 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were
 represented in the assembly. and a total of 24,564 genes were annotated
 for future functional genomics studies. We performed a candidate gene
 analysis to compare three genes among all three freshwater eel species
 and, congruent with the phylogenetic relationships, Japanese eel (A.
 japanica) exibited the most divergence. Overall, the sequenced genome
 presented in this study is a crucial addition to the presently available
 genetic tools to help guide future conservation efforts of Freshwater
 eels.
description: American_eel_annotation_filesIncluded is a compressed file containing a gff annotation file as well as blast results for all CDS regions.161025_american_eel_genome_annotation.tar.gz
DOI: 10.5061/dryad.8705
title: Data from: Shell geometry and habitat determination in extinct and extant turtles (Reptilia: Testudinata)

description: A number of means, including forelimb proportions and shell bone histology
 have been used to infer the paleoecology of extinct turtles. However, the
 height to width ratio of the shell (as a one-parameter shell model) has
 been dismissed because of its unreliability, and more complex aspects of
 shell geometry have generally been overlooked. Here we employ a more
 reliable, three-parameter geometric model of the shell outline in anterior
 view as a means to assess turtle paleoecology. The accuracy of predictions
 of extant turtle ecology based on our three-parameter shell model is
 comparable to that derived from forelimb proportions when distinguishing
 between three ecological classes (terrestrial, semi-aquatic and aquatic).
 Higher accuracy is obtained when distinguishing between two classes
 (terrestrial and non-terrestrial) since the contours of aquatic and
 semi-aquatic turtles are often very similar. Our model classifies
 Proterochersis robusta, a stem turtle from the Late Triassic of Germany,
 as non-terrestrial, and likely semi-aquatic. Our method, combined with
 inferences based on limb proportions, indicates a diverse range of
 ecotypes represented by Late Triassic stem turtles. This implies that the
 ecological diversification of stem-group turtles may have been rapid, or a
 substantial period of currently cryptic diversification preceded the first
 fossil appearance of the turtle stem lineage during the Late Triassic.
description: Benson et al turtle
 data
DOI: 10.5061/dryad.892f1
title: Data from: Detection of transient synchrony across oscillating receptors by the central electrosensory system of mormyrid fish

description: Recently, we reported evidence for a novel mechanism of peripheral sensory
 coding based on oscillatory synchrony. Spontaneously oscillating
 electroreceptors in weakly electric fish (Mormyridae) respond to
 electrosensory stimuli with a phase reset that results in transient
 synchrony across the receptor population (Baker et al., 2015). Here, we
 asked whether the central electrosensory system actually detects the
 occurrence of synchronous oscillations among receptors. We found that
 electrosensory stimulation elicited evoked potentials in the midbrain
 exterolateral nucleus at a short latency following receptor
 synchronization. Frequency tuning in the midbrain resembled peripheral
 frequency tuning, which matches the intrinsic oscillation frequencies of
 the receptors. These frequencies are lower than those in individual
 conspecific signals, and instead match those found in collective signals
 produced by groups of conspecifics. Our results provide further support
 for a novel mechanism for sensory coding based on the detection of
 oscillatory synchrony among peripheral receptors.
description: Evoked Potentials and
 EODsThe folder includes: 1.
 an excel file with data obtained from the mean evoked potentials, 2.
 Matlab files with the raw traces of the evoked potentials obtained for
 each fish, and 3. Matlab files with the electric organ discharges (EODs)
 of each species used to generate the power spectra.Velez_Carlson_eLIFE.zipMatlab CodesThis folder contains Matlab codes for generating and saving stimuli and for analyzing the evoked potentials