cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3xsj3txg2
title: LARS-WG stochastic weather generator

description: LARS-WG 6.0, a stochastic weather generator, is a computationally
 inexpensive downscaling tool to generate local scale climate scenarios
 based on global or regional climate models for impact assessments of
 climate change. LARS-WG has been used in more than 75 countries for
 research and education. The current version of LARS-WG incorporates
 climate projections from the CMIP5 ensemble used in the IPCC Fifth
 Assessment Report. LARS-WG has been well validated in diverse climates
 around the world.
DOI: 10.5061/dryad.pk0p2ngmz
title: Black box attack on machine learning assisted wide area monitoring and protection systems

description: The applications for wide area monitoring, protection, and control systems
 (WAMPC) at the control center, help with providing resilient, efficient,
 and secure operation of the transmission system of the smart grid. The
 increased proliferation of phasor measurement units (PMUs) in this space
 has inspired many prudent applications to assist in the process of
 decision making in the control centers. Machine learning (ML) based
 decision support systems have become viable with the availability of
 abundant high-resolution wide area operational PMU data. We propose a deep
 neural network (DNN) based supervisory protection and event diagnosis
 system and demonstrate that it works with very high degree of confidence.
 The system introduces a supervisory layer that processes the data streams
 collected from PMUs and detects disturbances in the power systems that may
 have gone unnoticed by the local monitoring and protection system. Then,
 we investigate compromise of the insights of this ML based supervisory
 control by crafting adversaries that corrupt the PMU data via minimal
 coordinated manipulation and identification of the spatio-temporal regions
 in the multidimensional PMU data in a way that the DNN classifier makes
 wrong event predictions.
description: This dataset contains images that represent PMU data described in
 the reference paper. Each image has a dimension of [300X20X3] comprising
 of 300 time points, 10 voltage and 10 frequency measurements, and 3
 fundamental color intensities. Each of the image represents the instance
 of a disturbance. We consider a disturbance pattern length of 5s, with 0.5
 s before the trigger and 4.5 s after the trigger. Voltage and frequency
 data streams from 10 PMUs at a sampling rate of 60 frames per second, were
 aggregated to form these pseudo color images. The data-set consisted of
 three sub-folders: 1. 344 instances of faults located in the sub-folder
 “DB_FLT” 2. 140 instances of loss of generation located in the sub-folder
 “DB_GNL” 3. 21 instances of synchronous motor switching events located in
 the sub-folder “DB_SMS”.
DOI: 10.5061/dryad.np5hqbzsg
title: Fitness effects of spontaneous mutation in a warming world

description: Spontaneous mutations fuel evolutionary processes and differ in
 consequence, but the consequences depend on the environment. Biophysical
 considerations of protein thermostability predict that warm temperatures
 may systematically increase the deleteriousness of mutation. We sought to
 test whether mutation reduced fitness more when measured in an environment
 that reflected climate change projections for temperature. We investigated
 the effects of spontaneous mutations on life history, size, and fitness in
 21 mutation accumulation lines and 12 control lines of Daphnia pulex at
 standard and elevated (+4℃) temperatures. Warmer temperature accelerated
 life history and reduced body length and clutch sizes. Mutation led to
 reduced mean clutch sizes and fitness estimates at both temperatures. We
 found no evidence of a systematic temperature-mutation interaction on
 trait means, although some lines showed evidence of beneficial mutation at
 one temperature and deleterious mutation at the other. However, trait
 variances are also influenced by mutation, and we observed increased
 variances due to mutation for most traits.  For variance of the
 intrinsic rate of increase and some reproductive traits, we found
 significant temperature-mutation interactions, with a larger increase due
 to mutation in the warmer environment. This suggests that selection on new
 mutations will be more efficient at elevated temperatures.
DOI: 10.5061/dryad.1ns1rn8t1
title: Phenotypic stability in scalar calcium of freshwater fish across a wide range of aqueous calcium availability in nature

description: Spatial environmental gradients can promote adaptive differences among
 conspecific populations as a result of local adaptation or phenotypic
 plasticity. Such divergence can be opposed by various constraints,
 including gene flow, limited genetic variation, temporal fluctuations, or
 developmental constraints. We focus on the constraint that can be imposed
 when some populations are found in locations characterized by low levels
 of an essential nutrient. We use scales of wild fish to investigate
 phenotypic effects of spatial variation in a potentially limiting nutrient
 – calcium. If scale calcium (we use “scalar” calcium for
 consistency with the physiology literature) simply reflects environmental
 calcium availability, we expect higher levels of scalar calcium in fish
 from calcium-rich water, compared to fish from calcium-poor water. To
 consider this “passive response” scenario, we analysed scalar calcium
 concentrations from three native fish species (Lepomis gibbosus, Percina
 caprodes, and Perca flavescens) collected at multiple sites across a
 dissolved calcium gradient in the Upper St. Lawrence River. Contradicting
 the “passive response" scenario, we did not detect strong or
 consistent relationships between scalar calcium and water calcium.
 Instead, for a given proportional increase in water calcium across the
 wide environmental gradient, the corresponding proportional change in
 scalar calcium was much smaller. We thus favor the alternative “active
 homeostasis” scenario, wherein fish from calcium-poor water are better
 able to uptake, mobilize, and deposit calcium than are fish from
 calcium-rich water. We further highlight the importance of
 studying functional traits, such as scales, in their natural setting as
 opposed to only laboratory studies.
DOI: 10.5061/dryad.2bvq83bpr
title: A linear time solution to the Labeled Robinson-Foulds Distance problem

description: Motivation: Comparing trees is a basic task for many purposes, and
 especially in phylogeny where different tree reconstruction tools may lead
 to different trees, likely representing contradictory evolutionary
 information. While a large variety of pairwise measures of similarity or
 dissimilarity have been developed for comparing trees with no information
 on internal nodes, very few address the case of inner node-labeled trees.
 Yet such trees are common; for instance reconciled gene trees have inner
 nodes labeled with the type of event giving rise to them, typically
 speciation or duplication. Recently, we proposed a formulation of the
 Labeled Robinson Foulds edit distance with edge extensions, edge
 contractions between identically labeled nodes, and node label flips.
 However, this distance proved difficult to compute, in particular because
 shortest edit paths can require contracting “good” edges, i.e. edges
 present in the two trees. Results: Here, we report on a different
 formulation of the Labeled Robinson Foulds edit distance — based on node
 insertion, deletion and label substitution — which we show can be computed
 in linear time. The new formulation also maintains other desirable
 properties: being a metric, reducing to Robinson Foulds for unlabeled
 trees and maintaining an intuitive interpretation. The new distance is
 computable for an arbitrary number of label types, thus making it useful
 for applications involving not only speciations and duplications, but also
 horizontal gene transfers and further events associated with the internal
 nodes of the tree. To illustrate the utility of the new distance, we use
 it to study the impact of taxon sampling on labeled gene tree inference,
 and conclude that denser taxon sampling yields better trees.
description: <strong>Experimental data</strong>
 The "ALF_Output" directory contains the results
 obtained from ALF with parameters specified in the paper, as well as
 additional files generated in the downstream analysis (see
 below) The "Partitions" directory contains
 one directory by partitioning of the 100 species from ALF in nested sets.
 Each contains three folder and a file. The summary.txt
 directory report which family are part of the nested set.
 The Allfamily directory contains the FASTA file of the 100 gene
 families generated with ALF, with only the species selected in the
 partition. The Aln directory contains the MSA for each
 gene family as generated with MAFFT with the selected species
 set The FTree directory contains the gene tree for each
 family as generated with FastTree with the selected species set
 The "Script" directory contains the files used to
 generated the data from the ALF directory, as well as downstream
 analysis
DOI: 10.5061/dryad.kd51c5b51
title: Data from: Morphology of western and semipalmated Sandpipers 1978-2020

description: Increasing predation danger can select for safety-enhancing modifications
 to prey morphology. We document multi-decade wing lengthening of a Pacific
 flyway migrant, the western sandpiper (Calidris mauri), and contrast this
 with contemporaneous wing shortening of the closely related semipalmated
 sandpiper (C. pusilla) on the Atlantic flyway. We measured &gt; 12,000
 southbound western sandpipers captured 1978–2020 at a major stopover site
 in British Columbia. Wing length increased at 0.074 mm y-1 (SE = 0.017; p
 &lt; 0.0003) for adults, and 0.087 mm y-1 (SE = 0.029; p &lt;
 0.007) for juveniles. These rates are of similarly large magnitude (4–5%
 overall), but opposite in direction, to the rate we previously reported
 for semipalmated sandpiper adults (-0.103 mm y-1). In both species, the
 change is specific to wings rather than being part of general body size
 change. We interpret both trends as responses to the ongoing strong
 increase of peregrine falcon (Falco peregrinus) populations since the
 mid-1970s, an important predator encountered by these species in
 contrasting ways during migration. Western sandpiper and peregrine
 migrations have temporal and spatial overlap. Longer wings enhance
 migratory speed and efficiency, enabling western sandpipers to decrease
 overlap by advancing to safer zones ahead of falcon passage. In contrast,
 semipalmated sandpipers primarily encounter peregrines as residents at
 migratory staging sites. Shorter wings improve acceleration and agility,
 helping migrants to escape attacks. Juvenile western sandpiper wing length
 also shows a component additive to the lengthening trend, shifting between
 years at 0.055 mm d-1 with the highly variable snowmelt date, with wings
 shorter following early springs. On the Pacific flyway, the timing of
 peregrine southward passage advances with snowmelt, increasing the
 relative exposure of juveniles to post-migratory resident peregrines. We
 interpret this annual wing length adjustment as an induced defense, made
 possible because snowmelt timing is a reliable cue to danger in the
 upcoming migration.
description: Capture and morphological measurement of breeding and migrating
 semipalmated and western Sandpipers. Trends and effects
 on annual variation were modeled with linear models.
DOI: 10.5061/dryad.5mkkwh757
title: Six-state amino acid recoding is not an effective strategy to offset compositional heterogeneity and saturation in phylogenetic analyses

description: Six-state amino acid recoding strategies are commonly applied to combat
 the effects of compositional heterogeneity and substitution saturation in
 phylogenetic analyses. While these methods have been endorsed from a
 theoretical perspective, their performance has never been extensively
 tested. Here, we test the effectiveness of 6-state recoding approaches by
 comparing the performance of analyses on recoded and non-recoded datasets
 that have been simulated under gradients of compositional heterogeneity or
 saturation. In our simulation analyses, non-recoding approaches
 consistently outperform 6-state recoding approaches. Our results suggest
 that 6-state recoding strategies are not effective in the face of high
 saturation. Further, while recoding strategies do buffer the effects of
 compositional heterogeneity, the loss of information that accompanies
 6-state recoding outweighs its benefits. In addition, we evaluate recoding
 schemes with 9, 12, 15, and 18 states and show that these consistently
 outperform 6-state recoding. Our analyses of other recoding schemes
 suggest that under conditions of very high compositional heterogeneity, it
 may be advantageous to apply recoding using more than 6 states, but we
 caution that applying any recoding should include sufficient
 justification. Our results have important implications for the more than
 90 published papers that have incorporated 6-state recoding, many of which
 have significant bearing on relationships across the tree of life.
description: To reproduce analyses, see the README file that is included with
 the alignments for instructions on how to integrate them into the GitHub
 repository associated with the data
 (https://github.com/josephryan/Hernandez_Ryan_2021_Recoding). NOTE: The 40
 million alignments with no induced compositional heterogeneity (used to
 generate null distributions) have not been included. The instructions for
 generating these alignments are included in the
 02-COMPOSITIONAL_HETEROGENEITY/01-NULL_DISTRIBUTION directory of the
 GitHub repository.
DOI: 10.5061/dryad.5qfttdz4h
title: Deconstructing incubation behaviour in response to ambient temperature over different timescales

description: Avian embryos need a stable thermal environment to develop optimally,
 while incubating females need to allocate time to self-maintenance off the
 nest. In species with female-only incubation, eggs are exposed to ambient
 temperatures that usually cool them down during female absences. The lower
 the ambient temperature the sooner females should return to re-warm the
 eggs. When incubation constraints ease at increasing ambient temperatures,
 females respond by increasing either incubation effort or self-maintenance
 time. These responses are population-dependent even within the same
 species; but it is uncertain whether they are caused by local
 environmental conditions or they are an artefact from limited datasets,
 different methodological approaches or the timescale over which incubation
 behaviour is measured. In this study, we collected incubation data from
 three Mediterranean Great TitParus major populations during three
 consecutive years. We measured the duration of each off- and on-bout
 event, used these variables to compute nest attentiveness at three
 different timescales (full incubation, daily, and hourly periods) and
 assessed the impact of ambient temperature on bout duration and nest
 attentiveness. We found that females maximized on-bout duration at
 different local temperatures, ranging from 10 to 20 ºC; but lengthened
 off-bouts linearly across a range of 0–38ºC in all three populations.
 These local differences translated into opposite linear nest attentiveness
 patterns at the full incubation scale: Females increased either incubation
 effort, longest on-bouts between 15-20ºC, or self-maintenance time,
 longest on-bouts at 10ºC. It was at daily and hourly periods when we
 detected non-linear nest attentiveness patterns, as expected from on-bout
 duration, peaking at different local ambient temperatures. Females first
 increased incubation effort up to a certain temperature value and then
 increased self-maintenance time at the highest ambient temperatures.
 Further research is needed to understand which factors are behind the
 turning points from one behaviour to the other.
DOI: 10.5061/dryad.nzs7h44r0
title: On the scaling and standardization of charcoal data in paleofire reconstructions

description: Understanding the biogeography of past and present fire events is
 particularly important in tropical forest ecosystems, where fire rarely
 occurs in the absence of human ignition. Open science databases have
 facilitated comprehensive and synthetic analyses of past fire activity,
 but charcoal datasets must be standardized (scaled) because of variations
 in measurement strategy, sediment type, and catchment size. 
 Here, we: i) assess how commonly used metrics of charcoal scaling perform
 on datasets from tropical forests; ii) introduce a new method called
 proportional relative scaling, which down-weights rare and infrequent
 fire; and iii) compare the approaches using charcoal data from four lakes
 in the Peruvian Amazon. We found that Z-score transformation and relative
 scaling (existing methods) distorted the structure of the charcoal peaks
 within the record, inflating the variation in small-scale peaks and
 minimizing the effect of large peaks. Proportional relative scaling
 maintained the structure of the original non-scaled data and contained
 zero values for the absence of fire. Proportional relative scaling
 provides an alternative scaling approach when the absence of fire is
 central to the aims of the research or when charcoal is infrequent and
 occurs in low abundances.
description: Charcoal was processed and analyzed from four lake sediments in
 the Peruvian Amazon. The charcoal data were standardized in three
 different ways: z-score transformation, relative scaling, and proportional
 relative scaling. See the methods section of the main article for an
 extended description of data collection, laboratory processing and
 analyses, and data standardization techniques.
description: The dataset contains four data files (one per lake) and a readme
 file to describe the data files.
DOI: 10.5061/dryad.2v6wwpzmp
title: Extreme home range sizes among Eurasian lynx at the northern edge of their biogeographic range

description: Eurasian lynx (Lynx lynx) have a wide distribution across Eurasia. The
 northern edge of this distribution is in Norway, where they reach up to 72
 degrees north. We conducted a study of lynx space use in this region from
 2007 to 2013 using GPS telemetry. The home range sizes averaged 2,606 (±
 438 SE) km2 for males (n=9 ranges) and 1,456 (± 179 SE) km2 for females
 (n=24 ranges). These are the largest home ranges reported for any large
 felid, and indeed are only matched by polar bears, arctic living wolves,
 and grizzly bears among all the Carnivora. The habitat occupied was almost
 entirely treeless alpine tundra, with home ranges only containing from 20
 to 25% of forest. These data have clear implications for the spatial
 planning of lynx management in the far north as the current management
 zones are located in unsuitable habitats and are not large enough to
 encompass individual lynx movements.
description: Home ranges are based on locations from GPS-collars fitted on
 Lynx. The different types of home range estimators are given in the
 file.
description: There are two CSV files, 1 containing home range sizes for all
 lynx with different range estimators and 1 containing overlap in home
 ranges between and within individuals based on the MCP 100% home range
 estimator.
DOI: 10.5061/dryad.pvmcvdnkd
title: Is phylogeographic congruence predicted by historical habitat stability, or ecological co-associations?

description: Comparative phylogeographic studies can uniquely distinguish idiosyncratic
 versus community-wide responses to past environmental change. However, to
 date, impacts of species interactions have been largely overlooked. Here
 we used non-genetic data to characterize two competing scenarios about
 expected levels of congruence among five saproxylic invertebrate species
 (i.e., a wood-feeding cockroach, termite and beetle; a predatory
 centipede, and a detritivorous millipede) from the southern Appalachians
 mountains—a topographically complex unglaciated landscape. Under one
 scenario, abiotic factors primarily drove species’ responses, with
 predicted congruence based on spatial overlap of climatically stable
 habitat areas estimated for each species via ecological niche modeling.
 The other scenario considered biotic factors to be most influential, with
 proxies for actual or potential direct interactions used to predict
 congruence. Analyses of mitochondrial and nuclear DNA sequence datasets
 for each species focused on four axes of comparison: the number and
 distribution of spatial-genetic clusters, phylogeographic structure,
 changes in long-term effective population size, and historical gene flow
 dynamics. Overall, we found stronger support for ecological
 co-associations scenario, suggesting an important influence of biotic
 factors in constraining or facilitating species’ responses to Pleistocene
 climatic cycles. However, there was an imperfect fit between this
 scenario’s predictions and outcomes of empirical data analyses. Thus, our
 conclusions are compelling, but tentative. This work advances comparative
 phylogeography by expanding the scope of inferences beyond abiotic
 drivers, and provides insights into the evolutionary history of a
 functionally important ecological community, within a globally recognized
 center of endemism.
description: DNA sequences for mitochondrial and nuclear loci were generated
 via Sanger sequencing using an Applied Biosystems 3730x Genetic Analyzer,
 performed by Yale University's DNA Analaysis Facilty on Science
 Hill.
DOI: 10.5061/dryad.gxd2547km
title: Data from: Predicting spatial patterns of Sindbis virus (SINV) infection risk in Finland using vector, host and environmental data

description: Pogosta disease is a mosquito-borne infection, caused by the Sindbis virus
 (SINV) with epidemics of febrile rash and arthritis in Northern Europe and
 South Africa. The virus is maintained in a transmission cycle between
 birds and mosquitoes. Resident grouse and migratory birds play a
 significant role as amplifying hosts and various mosquito species,
 including Aedes cinereus, Culex pipiens, Cx. torrentium and Culiseta
 morsitans are documented vectors. As specific treatments are not available
 for SINV infections and joint symptoms may persist, the public health
 burden is considerable in endemic areas. To predict the environmental and
 ecological suitability for SINV infections in Finland, we have applied a
 suite of geospatial and statistical modelling techniques to disease
 occurrence data. Using an ensemble approach, we first produced
 environmental suitability maps for potential SINV vectors in Finland.
 These suitability maps were then combined with host species and
 environmental data to identify the influential determinants for SINV
 infections, and to predict the risk of Pogosta disease in Finnish
 municipalities. This is the first study to utilise the spatial
 distribution of potential SINV vectors to predict the occurrence of
 Pogosta disease. Our predictions suggest that both the environmental
 suitability for vector species and the high risk of Pogosta disease are
 focused in geographically restricted areas. This provides evidence that
 presence of both SINV vector and host species can predict the occurrence
 of the disease. These results are essential for public health officials to
 inform risk assessments, and for future research to identify potential
 high-risk areas to prevent SINV infections.
description: This data includes all new data generated in
 the project, including the following: prediction maps for <i>Ae.
 cinereus</i>/<i>geminus</i>, <i>Cx.
 pipiens</i>/<i>torrentium, </i>and <i>Cs.
 morsitans</i> in Finland, model performance and variable importance
 comparison and predicted risk maps for Pogosta disease in
 Finland.