cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7q19c
title: Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

description: Environmental DNA (eDNA) is used to detect biodiversity by the capture,
 extraction, and identification of DNA shed to the environment. However,
 eDNA capture and extraction protocols vary widely across studies. This use
 of different protocols potentially biases detection results and could
 significantly hinder a reliable use of eDNA to detect biodiversity. We
 tested whether choice of eDNA capture and extraction protocols
 significantly influenced biodiversity detection in aquatic systems. We
 sampled lake and river water, captured and extracted eDNA using six
 combinations of different protocols with replication, and tested for the
 detection of four macroinvertebrate species. Additionally, using the same
 lake water technical replicates, we compared the effect of capture and
 extraction protocols on metabarcode detections of biodiversity using 16S
 for eubacteria and cytochrome c oxidase I (COI) for eukaryotes. Protocol
 combinations for capture and extraction of eDNA significantly influenced
 DNA yield and number of sequences obtained from next generation
 sequencing. We found significantly different detection rates of species
 ranging from zero percent to thirty-three percent. Differences in which
 protocol combinations produced the highest metabarcoded biodiversity were
 detected and demonstrate that different protocols are required for
 different biodiversity targets. Our results highlight that the choice of
 molecular protocols used for capture and extraction of eDNA from water can
 strongly affect biodiversity detection. Consideration of biases caused by
 choice of protocols should lead to a more consistent and reliable
 molecular workflow for repeatable and increased detection of biodiversity
 in aquatic communities.
description: FASTA file containing
 sequences for COIThis file contains the
 unique sequences used for taxonomic assignment against the nucleotide NCBI
 database. Sequences names are as they appear in the online supplemental
 Table A3.COI_l150.faFASTA file containing seqeunces for 16SThis file contains the unique sequences used for taxonomic assignment against the nucleotide NCBI database. Sequences names are as they appear in the online supplemental Table A2.16S_l250.fa
DOI: 10.5061/dryad.p2q52
title: Data from: AMAS: a fast tool for large alignment manipulation and computing of summary statistics

description: The amount of data used in phylogenetics has grown explosively in the
 recent years and many phylogenies are inferred with hundreds or even
 thousands of loci and many taxa. These modern phylogenomic studies often
 entail separate analyses of each of the loci in addition to multiple
 analyses of subsets of genes or concatenated sequences. Computationally
 efficient tools for handling and computing properties of thousands of
 single-locus or large concatenated alignments are needed. Here I present
 AMAS (Alignment Manipulation And Summary), a tool that can be used either
 as a stand-alone command-line utility or as a Python package. AMAS works
 on amino acid and nucleotide alignments and combines capabilities of
 sequence manipulation with a function that calculates basic statistics.
 The manipulation functions include conversions among popular formats,
 concatenation, extracting sites and splitting according to a pre-defined
 partitioning scheme, creation of replicate data sets, and removal of taxa.
 The statistics calculated include the number of taxa, alignment length,
 total count of matrix cells, overall number of undetermined characters,
 percent of missing data, AT and GC contents (for DNA alignments), count
 and proportion of variable sites, count and proportion of parsimony
 informative sites, and counts of all characters relevant for a nucleotide
 or amino acid alphabet. AMAS is particularly suitable for very large
 alignments with hundreds of taxa and thousands of loci. It is
 computationally efficient, utilizes parallel processing, and performs
 better at concatenation than other popular tools. AMAS is a Python 3
 program that relies solely on Python’s core modules and needs no
 additional dependencies. AMAS source code and manual can be downloaded
 from http://github.com/marekborowiec/AMAS/ under GNU General Public
 License.
description: Suppl_alnsThis folder contains three alignments: 'AMAS_j2013.fas', 'FcC_j2013.fas', and 'Phyut_j2013.nex' concatenated respectively by AMAS, FASconCAT-G, and Phyutility. The 'summary.txt' file contains summaries of these three alignments, as calculated by AMAS, showing that they are identical. 'FcC_info.xls' is the summary calculated on j2013 data set by FASconCAT-G.
DOI: 10.5061/dryad.c128h
title: Data from: Rates of morphological evolution are heterogeneous in Early Cretaceous birds

description: The Early Cretaceous is a critical interval in the early history of birds.
 Exceptional fossils indicate that important evolutionary novelties such as
 a pygostyle and a keeled sternum had already arisen in Early Cretaceous
 taxa, bridging much of the morphological gap between Archaeopteryx and
 crown birds. However, detailed features of basal bird evolution remain
 obscure because of both the small sample of fossil taxa previously
 considered and a lack of quantitative studies assessing rates of
 morphological evolution. Here we apply a recently available phylogenetic
 method and associated sensitivity tests to a large data matrix of
 morphological characters to quantify rates of morphological evolution in
 Early Cretaceous birds. Our results reveal that although rates were highly
 heterogeneous between different Early Cretaceous avian lineages,
 consistent patterns of significantly high or low rates were harder to
 pinpoint. Nevertheless, evidence for accelerated evolutionary rates is
 strongest at the point when Ornithuromorpha (the clade comprises all
 extant birds and descendants from their most recent common ancestors)
 split from Enantiornithes (a diverse clade that went extinct at the
 end-Cretaceous), consistent with the hypothesis that this key split opened
 up new niches and ultimately led to greater diversity for these two
 dominant clades of Mesozoic birds.
description: phylogenetic methods and
 sensitivity testsComplete data used in
 Wang and Graeme's paper, including following files: data matrix of
 Mesozoic birds, age of the terminal taxa, most parsimonious trees, code in
 R analysis, and the complete results of the sensitive
 tests.Dryad.rar
DOI: 10.5061/dryad.1fq87
title: Data from: Studying developmental variation with Geometric Morphometric Image Analysis (GMIA)

description: The ways in which embryo development can vary across individuals of a
 population determine how genetic variation translates into adult
 phenotypic variation. The study of developmental variation has been
 hampered by the lack of quantitative methods for the joint analysis of
 embryo shape and the spatial distribution of cellular activity within the
 developing embryo geometry. By drawing from the strength of geometric
 morphometrics and pixel/voxel-based image analysis, we present a new
 approach for the biometric analysis of two-dimensional and
 three-dimensional embryonic images. Well-differentiated structures are
 described in terms of their shape, whereas structures with diffuse
 boundaries, such as emerging cell condensations or molecular gradients,
 are described as spatial patterns of intensities. We applied this approach
 to microscopic images of the tail fins of larval and juvenile rainbow
 trout. Inter-individual variation of shape and cell density was found
 highly spatially structured across the tail fin and temporally dynamic
 throughout the investigated period.
description: Images &
 landmarksMicroscopic images of
 the tail fins of 20 rainbow trout specimens (Oncorhynchus mykiss). The
 fish were collected from one hatchery in the year 2000. Specimens were
 euthanized by overdose of MS222, fixed in buffered formalin, and stored in
 70% ethanol. Seven of them were fixed at 21 days post fertilization (dpf),
 eight at 40 dpf, and five at 56 dpf. In 2013, the specimens were
 transferred into distilled water before they were stained with Mayer’s
 hematoxylin for 10 minutes. All images were taken under identical light
 conditions and standardized specimen orientation with a 5x magnification.
 Four anatomical landmarks and 95 semilandmarks were recorded on each of
 the 20 images using the software TPSdig (James Rohlf). The resulting raw
 landmark coordinates are given in the file
 "landmarks.tps".Images_landmarks.zip
DOI: 10.5061/dryad.5vv37
title: Data from: Is the sky the limit? On the expansion threshold of a species' range

description: More than 100 years after Grigg’s influential analysis of species’
 borders, the causes of limits to species’ ranges still represent a puzzle
 that has never been understood with clarity. The topic has become
 especially important recently as many scientists have become interested in
 the potential for species’ ranges to shift in response to climate
 change—and yet nearly all of those studies fail to recognise or
 incorporate evolutionary genetics in a way that relates to theoretical
 developments. I show that range margins can be understood based on just
 two measurable parameters: (i) the fitness cost of dispersal—a measure of
 environmental heterogeneity—and (ii) the strength of genetic drift, which
 reduces genetic diversity. Together, these two parameters define an
 ‘expansion threshold’: adaptation fails when genetic drift reduces genetic
 diversity below that required for adaptation to a heterogeneous
 environment. When the key parameters drop below this expansion threshold
 locally, a sharp range margin forms. When they drop below this threshold
 throughout the species’ range, adaptation collapses everywhere, resulting
 in either extinction or formation of a fragmented metapopulation. Because
 the effects of dispersal differ fundamentally with dimension, the second
 parameter—the strength of genetic drift—is qualitatively different
 compared to a linear habitat. In two-dimensional habitats, genetic drift
 becomes effectively independent of selection. It decreases with
 ‘neighbourhood size’—the number of individuals accessible by dispersal
 within one generation. Moreover, in contrast to earlier predictions, which
 neglected evolution of genetic variance and/or stochasticity in two
 dimensions, dispersal into small marginal populations aids adaptation.
 This is because the reduction of both genetic and demographic
 stochasticity has a stronger effect than the cost of dispersal through
 increased maladaptation. The expansion threshold thus provides a novel,
 theoretically justified, and testable prediction for formation of the
 range margin and collapse of the species’ range.
description: Species Range -
 Mathematica Code and ExampleMathematica code and a
 working example of the simulations, Figures with dataSpeciesRangeMathematicaCodeExampleFigures.cdf
DOI: 10.22003/xfel.eu-data-900530-00
title: SHG commissioning 2025-II
DOI: 10.5061/dryad.01br7
title: Data from: Perception of odors linked to precise timing in the olfactory system

description: While the timing of neuronal activity in the olfactory bulb (OB) relative
 to sniffing has been the object of many studies, the behavioral relevance
 of timing information generated by patterned activation within the bulbar
 response has not been explored. Here we show, using sniff-triggered,
 dynamic, 2-D, optogenetic stimulation of mitral/tufted cells, that virtual
 odors that differ by as little as 13 ms are distinguishable by mice.
 Further, mice are capable of discriminating a virtual odor movie based on
 an optically imaged OB odor response versus the same virtual odor devoid
 of temporal dynamics—independently of the sniff-phase. Together with
 studies showing the behavioral relevance of graded glomerular responses
 and the response timing relative to odor sampling, these results imply
 that the mammalian olfactory system is capable of very high transient
 information transmission rates.
description: ArchiveData on all stimuli and mouse performance
DOI: 10.22003/xfel.eu-data-900531-00
title: SCS commissioning
DOI: 10.5061/dryad.h5c80
title: Data from: Evaluation of sampling frequency, window size and sensor position for classification of sheep behaviour

description: Automated behavioural classification and identification through sensors
 has the potential to improve health and welfare of the animals. Position
 of a sensor, sampling frequency and window size of segmented signal data
 has a major impact on classification accuracy in activity recognition and
 energy needs for the sensor, yet, there are no studies in precision
 livestock farming that have evaluated effect of all these factors
 simultaneously. The aim of this study was to evaluate the effects of
 position (ear and collar), sampling frequency (8Hz, 16Hz and 32 Hz) of a
 tri-axial accelerometer and gyroscope sensor and window size (3s, 5s and
 7s) of on the classification of important behaviours in sheep such as
 lying, standing and walking. Behaviours were classified using a random
 forest approach with forty-four feature characteristics. The best
 performance for walking, standing and lying classification in sheep
 (accuracy 95%, F-score 91-97%) was obtained using combination of 32Hz, 7s
 and 32Hz, 5s for both ear and collar sensors, although, results obtained
 with 16Hz and 7s window were comparable with accuracy of 91-93% and
 F-score 88-95%. Energy efficiency was best at a 7s window. This suggests
 that sampling at 16Hz with 7s window will offer benefits in a real-time
 behavioural monitoring system for sheep due to reduced energy needs.
description: All features with mixed
 windowsThe folder contains
 feature characteristics used for the classification of walking, standing
 and lying in sheep. The different files contain either collar or ear data.
 The first column at the files indicates if the window was mixed(1) or
 non-mixed. The column "Fs" represents the frequency. The column
 with header "ws" represents the window size. The column with
 header "WSL" represents the ground truth with walking (1),
 standing(2) and lying(3).All_features_with_mixed_windows.zip
DOI: 10.5061/dryad.7rn79
title: Data from: Water-borne pharmaceuticals reduce phenotypic diversity and response capacity of natural phytoplankton communities

description: Chemical micropollutants occur worldwide in the environment at low
 concentrations and in complex mixtures, and how they affect the ecology of
 natural systems is still uncertain. Dynamics of natural communities are
 driven by the interaction between individual organisms and their growth
 environment, which is mediated by the organisms' expressed phenotypic
 traits. We tested whether exposure to a mixture of 12 pharmaceuticals and
 personal care products (PPCP) influences phenotypic trait diversity in
 lake phytoplankton communities and their ability to regulate biomass
 production to fit environmental changes (response capacity). We exposed
 natural phytoplankton assemblages to three mixture levels in permeable
 microcosms maintained at three depths in a eutrophic lake for one week,
 during which the environmental conditions were fluctuating. We studied
 individual-level traits, phenotypic diversity and community biomass. PPCP
 reduced individual-level trait variance and overall community phenotypic
 diversity, but maintained higher standing phytoplankton biomass compared
 to untreated controls. Estimated effect sizes of PPCP on traits and
 community properties were very large (partial Eta-squared &gt; 0.15).
 The PPCP mixture antagonistically interacted with the natural
 environmental gradient in habitats offered by different depths and, at
 concentrations comparable to those in waste-water effluents, prevented
 communities from converging to the same phenotypic structure and total
 biomass of unexposed controls. We show that micropollutants can alter
 individual-level trait diversity of lake phytoplankton communities and
 therefore their capacity to respond to natural environmental gradients,
 potentially affecting aquatic ecosystem processes.
description: Data_&_DOE_analysis_codeThe archive (.zip) includes the cleaned flow-cytometry data, the final summary table used for the analysis of the experiment and the SPSS code for the GLM.
DOI: 10.5061/dryad.p11s3
title: Data from: Sperm allocation in relation to female size in a semelparous salmonid

description: To maximize reproductive success, males have to adaptively tailor their
 sperm expenditure in relation to the quality of potential mates because
 they require time to replenish their sperm supply for subsequent mating
 opportunities. Therefore, in mating contexts where males must choose among
 females in a short period of time, as is the case with semelparous species
 (which die after one intensely competitive short duration breeding
 season), selection on sperm allocation can be expected to be a powerful
 selective agent that shapes the male reproductive success. We
 quantitatively investigated sperm allocation patterns in chum salmon in
 relation to perceived female quality by developing a novel method for
 determining the amount of sperm allocated per ejaculate during spawning
 bouts. We examined the relationship between sperm expenditure and the body
 size of paired females (a proxy of egg number and egg quality) in the
 absence of male–male competition in an experimental channel. The estimated
 amount of sperm released per spawning event was positively correlated with
 the size of paired females. However, the number of spawning events a
 female participated in, which reduces the number of eggs she spawns in
 each subsequent bout, did not affect this relationship. These results
 provide support for predictions arising from the sperm allocation
 hypothesis, male salmon do economize their sperm expenditure in accordance
 with paired female body size as predicted for their first spawning event,
 but males overestimate or are unable to assess the quality of females
 beyond size and provide more sperm than they should in theory when paired
 with a female that spawned previously. Overall, the observed sperm
 allocation pattern in chum salmon appears to be adapted to maximize
 reproductive success assuming female size is an honest indicator of
 quality, although temporal changes in a female's quality during a
 reproductive season should be considered when examining sperm allocation
 strategies.
description: Sway acceleration data
 at gamete release in 2011Acceleration_at_gamete_
 release_2011.txtSway acceleration data
 at gamete release in 2012Acceleration_at_gamete_
 release_2012.txtSway acceleration data
 at gamete release in 2013Acceleration_at_gamete_
 release_2013.txt
DOI: 10.5061/dryad.7174h
title: Data from: Vegetation recovery in tidal marshes reveals critical slowing down under increased inundation

description: A declining rate of recovery following disturbance has been proposed as an
 important early warning for impending tipping points in complex systems.
 Despite extensive theoretical and laboratory studies, this ‘critical
 slowing down’ remains largely untested in the complex settings of
 real-world ecosystems. Here, we provide both observational and
 experimental support of critical slowing down along natural stress
 gradients in tidal marsh ecosystems. Time series of aerial images of
 European marsh development reveal a consistent lengthening of recovery
 time as inundation stress increases. We corroborate this finding with
 transplantation experiments in European and North American tidal marshes.
 In particular, our results emphasize the power of direct observational or
 experimental measures of recovery over indirect statistical signatures,
 such as spatial variance or autocorrelation. Our results indicate that the
 phenomenon of critical slowing down can provide a powerful tool to probe
 the resilience of natural ecosystems.
description: Data Bundle Nature
 CommunicationsData bundle including
 code supporting the publication: van Belzen, J., van de Koppel,, J.,
 Kirwan, M.L., van der Wal, D., Herman, P.M.J., Dakos, V., Kefi, S.,
 Scheffer, M., Guntenspergen, G.R., Bouma, T.J. (2017). Vegetation recovery
 in tidal marshes reveals critical slowing down under increased inundation.
 Nature CommunicationsData Bundle
 NCOMMS.zip
DOI: 10.5061/dryad.fj0qj
title: Data from: Rewiring of embryonic glucose metabolism via suppression of pfk-1/aldolase during mouse chorioallantoic branching

description: Adapting the energy metabolism state to changing bioenergetic demands is
 essential for mammalian development accompanying massive cell
 proliferation and cell differentiation. However, it remains unclear how
 developing embryos meet the changing bioenergetic demands during the
 chorioallantoic branching (CB) stage when the maternal-fetal exchange of
 gases and nutrients is promoted. In this study, using metabolome analysis
 with mass-labeled glucose, we found that developing embryos redirected
 glucose carbon flow into the pentose phosphate pathway (PPP) via
 suppression of the key glycolytic enzymes PFK-1 and aldolase during CB.
 Concomitantly, embryos had increases in lactate pool size and in the
 fractional contribution of glycolysis to lactate biosynthesis. Imaging
 mass spectrometry (IMS) visualized lactate-rich tissues, such as the
 dorsal or posterior neural tube, somites, and head mesenchyme.
 Furthermore, we found that the heterochronic gene Lin28a could act as a
 regulator of the metabolic changes observed during CB. Perturbation of
 glucose metabolism rewiring by suppressing Lin28a downregulation resulted
 in perinatal lethality. Thus, our work demonstrates that developing
 embryos rewire glucose metabolism following CB for normal development.
description: E8.5 mouse
 embryo_1Data of DNA microarray
 analysis of E8.5 mouse embryo (whole body)120205WE_E85_252665513563.txtE8.5 mouse embryo_2Data of DNA microarray analysis of E8.5 mouse embryo (whole body)120325WE_E85_252665513563.txtE8.5 mouse embryo_3Data of DNA microarray analysis of E8.5 mouse embryo (whole body)120325WE_E85_252665513563_2.txtE9.5 mouse embryo_1Data of DNA microarray analysis of E9.5 mouse embryo (whole body)120205WE_E95_252665513563.txtE9.5 mouse embryo_2Data of DNA microarray analysis of E9.5 mouse embryo (whole body)120325WE_E95_252665513563.txtE9.5 mouse embryo_3Data of DNA microarray analysis of E9.5 mouse embryo (whole body)120325WE_E95_252665513563_2.txtE10.5 mouse embryo_1Data of DNA microarray analysis of E10.5 mouse embryo (whole body)120205WE_E105_252665513563.txtE10.5 mouse embryo_2Data of DNA microarray analysis of E10.5 mouse embryo (whole body)120325WE_E105_252665513563.txtE10.5 mouse embryo_3Data of DNA microarray analysis of E10.5 mouse embryo (whole body)120325WE_E105_252665513563_2.txt