cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.121s23b
title: Data from: Objective estimation of sensory thresholds based on neurophysiological parameters

description: Reliable determination of sensory thresholds is the holy grail of signal
 detection theory. However, there exists no assumption-independent gold
 standard for the estimation of thresholds based on neurophysiological
 parameters, although a reliable estimation method is crucial for both
 scientific investigations and clinical diagnosis. Whenever it is
 impossible to communicate with the subjects, as in studies with animals or
 neonates, thresholds have to be derived from neural recordings or by
 indirect behavioral tests. Whenever the threshold is estimated based on
 such measures, the standard approach until now is the subjective
 setting—either by eye or by statistical means—of the threshold to the
 value where at least a “clear” signal is detectable. These measures are
 highly subjective, strongly depend on the noise, and fluctuate due to the
 low signal-to-noise ratio near the threshold. Here we show a novel method
 to reliably estimate physiological thresholds based on neurophysiological
 parameters. Using surrogate data we demonstrate that fitting the responses
 to different stimulus intensities with a hard sigmoid function, in
 combination with subsampling, provides a robust threshold value as well as
 an accurate uncertainty estimate. This method has no systematic dependence
 on the noise and does not even require samples in the full dynamic range
 of the sensory system. We prove that this method is universally applicable
 to all types of sensory systems, ranging from somatosensory stimulus
 processing in the cortex to auditory processing in the brain stem.
description: Schilling 2019
 DataA
 zip folder with the data and python code for all figures of the
 publication (including readme files).Schilling2019.zip
DOI: 10.5061/dryad.s6v210k
title: Data from: Integrating life history traits into predictive phylogeography

description: Predictive phylogeography seeks to aggregate genetic, environmental and
 taxonomic data from multiple species in order to make predictions about
 unsampled taxa using machine-learning techniques such as Random Forests.
 To date, organismal trait data have infrequently been incorporated into
 predictive frameworks due to difficulties inherent to the scoring of trait
 data across a taxonomically broad set of taxa. We refine predictive
 frameworks from two North American systems, the inland temperate
 rainforests of the Pacific Northwest (PNW) and the Southwestern Aridlands
 (SWAL), by incorporating a number of organismal trait variables. Our
 results indicate that incorporating life history traits as predictor
 variables improves the performance of the supervised machine-learning
 approach to predictive phylogeography, especially for the SWAL system, in
 which predictions made from only taxonomic and climate variables meets
 only moderate success. In particular, traits related to reproduction
 (e.g., reproductive mode; clutch size) and trophic level appear to be
 particularly informative to the predictive framework. Predictive
 frameworks offer an important mechanism for integration of organismal
 trait, environmental data, and genetic data in phylogeographic studies.
description: SAL_MLS_August08_2018_FullDataset_forRFSouthwestern Arid Lands DataPNW_MLS_August06_2018_FullDataset_forRFPacific Northwest DataPNW_BuildRFR script for Pacific Northwest AnalysisSAL_BuildRF_noneotoma_nofuscusR script for Southwestern Arid Lands Analysis
DOI: 10.5061/dryad.r86c7f3
title: Data from: Seasonal patterns in species diversity across biomes

description: A conspicuous Season-Diversity Relationship (SDR) can be seen in seasonal
 environments, often with a defined peak in active species diversity in the
 growing season. We ask is this a general pattern and are other patterns
 are possible? In addition, we ask what is the ultimate cause of this
 pattern and can we understand it using existing ecological theory? To
 accomplish this task, we assembled a global database on changes in species
 diversity through time in seasonal environments for different taxa and
 habitats and also conducted a modeling study in an attempt to replicate
 observed patterns. Our global database includes terrestrial and aquatic
 habitats, temperate, tropical, and polar environments, and taxa from
 disparate groups including vertebrates, insects, and plankton. We
 constructed nine alternative models that vary in assumptions on type of
 seasonal forcing, responses to that forcing, species niches, and types of
 species interactions. We found that most guilds of species exhibit a
 repeatable Season-Diversity Relationship (SDR) across years. For north
 temperate ecosystems, active species diversity generally peaks mid-year.
 The peak for a guild is generally more pronounced in terrestrial habitats
 than aquatic habitats and more pronounced in temperate and polar regions
 than the tropics. We now have evidence that at least several different
 habitat and taxa types are likely to have multiple peaks in diversity in a
 year, for example guilds of both aquatic microbes and desert vertebrates
 can show a bimodal or multimodal SDR. We compared all nine candidate
 models in their ability to explain the patterns and match their
 assumptions to the data. Some performed considerably better than others in
 being able to match the different patterns. We conclude that a model that
 includes both temperature niches and environmental feedbacks is necessary
 to explain the different season-diversity relationships. We use such a
 model to make predictions on how the SDR could be impacted by climate
 change. More effort should be put into documenting and understanding
 baseline seasonal patterns in diversity in order to predict future
 responses to global change.
description: Mellard_SDR_all_dataData used to analyze seasonal patterns in species diversity across biomes
DOI: 10.5061/dryad.2nc0bn1
title: Data from: Species’ range dynamics affect the evolution of spatial variation in plasticity under environmental change

description: While clines in environmental tolerance and phenotypic plasticity along a
 single species' range have been reported repeatedly and are of
 special interest in the context of adaptation to environmental changes, we
 know little about their evolution. Recent empirical findings in ectotherms
 suggest that processes underlying dynamic species' ranges can give
 rise to spatial differences in environmental tolerance and phenotypic
 plasticity within species. We used individual-based simulations to
 investigate how plasticity and tolerance evolve in the course of three
 scenarios of species' range shifts and range expansions on
 environmental gradients. We found that regions of a species' range
 which experienced a longer history or larger extent of environmental
 change generally exhibited increased plasticity or tolerance. Such regions
 may be at the trailing edge when a species is tracking its ecological
 niche in space (e.g., in a climate change scenario) or at the front edge
 when a species expands into a new habitat (e.g., in an expansion/invasion
 scenario). Elevated tolerance and plasticity in the distribution center
 was detected when asymmetric environmental change (e.g., polar
 amplification) led to a range expansion. However, tolerance and plasticity
 clines were transient and slowly flattened out after range dynamics
 because of genetic assimilation.
description: Nemo_ini_filesNemo_summaryDataReadMe
DOI: 10.5061/dryad.sp2ft6s
title: Data from: Rapid shifts in the thermal sensitivity of growth but not development rate causes temperature-size response variability during ontogeny in arthropods

description: Size at maturity in ectotherms commonly declines with warming. This
 near-universal phenomenon, formalised as the temperature-size rule, has
 been observed in over 80% of tested species, from bacteria to fish. The
 proximate cause has been attributed to the greater temperature dependence
 of development rate than growth rate, causing individuals to develop
 earlier but mature smaller in the warm. However, few studies have examined
 the ontogenetic progression of the temperature-size response at high
 resolution. Using marine planktonic copepods, we experimentally determined
 the progression of the temperature-size response over ontogeny.
 Temperature-size responses were not generated gradually from egg to adult,
 contrary to the predictions of a naïve model in which development rate was
 assumed to be more temperature-dependent than growth rate, and the
 difference in the temperature dependence of these two rates remained
 constant over ontogeny. Instead, the ontogenetic progression of the
 temperature-size response in experimental animals was highly episodic,
 indicating rapid changes in the extent to which growth and development
 rates are thermally decoupled. The strongest temperature-size responses
 occurred temporally mid-way through ontogeny, corresponding with the point
 at which individuals reached between ~5- 25% of their adult mass. Using
 the copepod Oithona nana, we show that the temperature-dependence of
 growth rate varied substantially throughout ontogeny, whereas the
 temperature dependence of development rate remained constant. The
 temperature-dependence of growth rate even exceeded that of development
 rate in some life stages, leading to a weakening of the temperature-size
 response. Our analyses of arthropod temperature-size responses from the
 literature, including crustaceans and insects, support these conclusions
 more broadly. Overall, our findings provide a better understanding of how
 the temperature-size rule is produced over ontogeny. Whereas we find
 support for the generality of developmental rate isomorphy in arthropods
 (shared temperature dependence of development rate across life stages),
 this concept should not apply to growth rates.
description: Data Set
 S1Raw
 stage-specific body size data for the marine planktonic copepod species
 used in this study.
DOI: 10.5061/dryad.8h36t01
title: Data from: A hierarchical Bayesian approach for handling missing classification data

description: Ecologists use classifications of individuals in categories to understand
 composition of populations and communities. These categories might be
 defined by demographics, functional traits, or species. Assignment of
 categories is often imperfect, but frequently treated as observations
 without error. When individuals are observed but not classified, these
 “partial” observations must be modified to include the missing data
 mechanism to avoid spurious inference. We developed two hierarchical
 Bayesian models to overcome the assumption of perfect assignment to
 mutually exclusive categories in the multinomial distribution of
 categorical counts, when classifications are missing. These models
 incorporate auxiliary information to adjust the posterior distributions of
 the proportions of membership in categories. In one model, we use an
 empirical Bayes approach, where a subset of data from one year serves as a
 prior for the missing data the next. In the other approach, we use a small
 random sample of data within a year to inform the distribution of the
 missing data. We performed a simulation to show the bias that occurs when
 partial observations were ignored and demonstrated the altered inference
 for the estimation of demographic ratios. We applied our models to
 demographic classifications of elk (Cervus elaphus nelsoni) to demonstrate
 improved inference for the proportions of sex and stage classes. We
 developed multiple modeling approaches using a generalizable nested
 multinomial structure to account for partially observed data that were
 missing not at random for classification counts. Accounting for
 classification uncertainty is important to accurately understand the
 composition of populations and communities in ecological studies.
description: Data from: A
 hierarchical Bayesian approach for handling missing classification
 dataDatasets consist of
 classifications and counts of elk in Rocky Mountain National Park, and
 Estes Valley, CO. Data are separated into CSV files by each year of the
 study, except aggregated ground counts for the entire study. Other
 datasets include year separated transect level group classification
 counts, and the auxiliary data from yearling and adult female groups
 isolated from the overall transect level group counts.Data_Ketz.zip
DOI: 10.5061/dryad.4q3d25m
title: Data from: A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India

description: The Western Ghats (WG) is an escarpment on the west coast of Peninsular
 India, housing one of the richest assemblages of frogs in the world, with
 three endemic families. Here, we report the discovery of a new ancient
 lineage from a high-elevation massif in the Wayanad Plateau of the
 southern WG. Phylogenetic analysis reveals that the lineage belongs to
 Natatanura and clusters with Nyctibatrachidae, a family endemic to the
 WG/Sri Lanka biodiversity hotspot. Based on geographic distribution,
 unique morphological traits, deep genetic divergence, and phylogenetic
 position that distinguishes the lineage from the two nyctibatrachid
 subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae
 Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae
 subfam. nov. (endemic to the WG, Peninsular India), and describe a new
 genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp.
 nov. The discovery of this species adds to the list of deeply divergent
 and monotypic or depauperate lineages with narrow geographic ranges in the
 southern massifs of the WG. The southern regions of the WG have long been
 considered geographic and climatic refugia, and this new relict lineage
 underscores their evolutionary significance. The small range of this
 species exclusively outside protected areas highlights the significance of
 reserve forest tracts in the WG in housing evolutionary novelty. This
 reinforces the need for intensive sampling to uncover new lineages and
 advance our understanding of the historical biogeography of this ancient
 landmass.
description: Amphibia_New_India_DryadPartition file describing GTRGAMMA model partitions from PartitionFinder2 for RAxML analysis.Amphibia_New_India_DryadPHYLIP file containing 15-gene, 4,063-taxon, 15,259bp alignment of DNA sequences.Amphibia_New_India_SHL_DryadNEWICK-format string containing tree file resulting from ML analysis of the alignment and model file.
DOI: 10.5061/dryad.pt70k51
title: Data from: Acoustic emissions of Sorex unguiculatus (Mammalia: Soricidae): assessing the echo-based orientation hypothesis

description: Shrew species have been proposed to utilize an echo-based orientation
 system to obtain additional acoustic information while surveying their
 environments. This system has been supported by changes in vocal emission
 rates when shrews encounter different habitats of varying complexity,
 although detailed acoustic features in this system have not been reported.
 In this study, behavioral experiments were conducted using the long-clawed
 shrew (Sorex unguiculatus) to assess this orientation system. Three
 experimental conditions were set, two of which contained obstacles.
 Short-click, noisy, and different types of tonal calls in the
 audible-to-ultrasonic frequency range were recorded under all experimental
 conditions. The results indicated that shrews emit calls more frequently
 when they are facing obstacles or exploring the experimental environment.
 Shrews emitted clicks and several different types of tonal calls while
 exploring, and modified the use of different types of calls for varying
 behavior. Furthermore, shrews modified the dominant frequency and duration
 of squeak calls for different types of obstacles, i.e., plants and acrylic
 barriers. The vocalizations emitted at short interpulse intervals could
 not be observed when shrews approached these obstacles. These results are
 consistent with the echo-based orientation hypothesis according to which
 shrews use a simple echo-orientation system to obtain information from
 their surrounding environments, although further studies are needed to
 confirm this hypothesis.
description: Acoustic features of
 Sorex unguiculatusThe file includes two
 sheets.(1) Acoustic feature of calls: Acoustic feature such as call
 duration and mean dominant frequency of calls emitted by shrews;(2) Number
 of calls: The number of calls emitted by shrews.shrews.xls
DOI: 10.5061/dryad.6760md8
title: Data from: Fossorial Damaraland mole rats do not exhibit a blunted hypercapnic ventilatory response

description: Damaraland mole rats (DMRs, Fukomys damarensis) are a eusocial fossorial
 species that spend the majority of their life in densely-populated
 underground burrows, in which they likely experience intermittent periods
 of elevated CO2 (i.e., hypercapnia). The primary physiological response to
 hypercapnia in most mammals is to increase depth and rate of breathing
 (i.e., hyperpnea), but this response is often blunted in species that
 inhabit hypercapnic environments. In their natural habitat, DMRs
 putatively experience a gaseous environment ranging from normocapnic (0.1%
 CO¬2) to hypercapnic (6.0% CO2) conditions (Roper et al., 2001). As such,
 we hypothesized that DMRs would exhibit blunted hypercapnic ventilatory
 and metabolic responses, relative to those of non-fossorial rodent
 species. To test this hypothesis, we exposed awake, freely behaving DMRs
 to normoxic normocapnia (21% O2, 0% CO2, balance N2) or graded normoxic
 hypercapnia (21% O2, 0, 2, 5, 7 and 10% CO2, balance N2), and measured
 ventilation and metabolism using whole-body plethysmography and indirect
 calorimetry, respectively. We found that ventilation and metabolism were
 unchanged during prolonged normocapnia, whereas during graded hypercapnia,
 ventilation was elevated at 2% CO2 and above. As a result, O2 extraction
 efficiency at the lungs decreased with increasing hyperpnea. Conversely,
 metabolic rate did not increase until 10% CO2, presumably due to the
 metabolic cost of hyperpnea. Taken together, our results suggest that
 despite their fossorial lifestyle, DMRs do not exhibit adaptations in
 their ventilatory or metabolic responses to environmental hypercapnia.
description: Hypercapnia
 TrialsData was collected from
 nine Damaraland mole rats in laboratory conditions, using Labchart
 software. Animals were exposed to 1-hr stages of 0, 2, 5, 7, 10% CO2, 21%
 O2, balance N2. Abbreviations in data files: % O2 - % outflowing O2, % CO2
 - % outflowing CO2, BL - pressure deflections adjusted for baseline drift
 throughout trial, Neg Int - Integration of all pressure values below zero;
 -BL - BL data * -1Normocapnia
 trialsData was collected from
 nine Damaraland mole rats in laboratory conditions, using Labchart
 software. Animals were exposed to 5 hrs of 0% CO2, 21% O2, balance N2.
 Abbreviations in data files: % O2 - % outflowing O2; % CO2 - % outflowing
 CO2; BL - pressure deflections adjusted for baseline drift throughout
 trial; Neg Int - Integration of all pressure values below zero; -BL - BL
 data * -1
DOI: 10.5061/dryad.1mv3348
title: Data from: Identifying ecological drivers of interspecific variation in song complexity in songbirds (Passeriformes, Passeri)

description: A diversity of selective pressures and stochastic processes have likely
 created substantial variation in song structure, creating difficulties in
 quantifying the influence of specific ecological factors. This problem is
 further compounded by differences in study taxa and methods of data
 analysis between studies. Large comparative studies offer the potential to
 mitigate some of these methodological difficulties by maximizing the power
 of statistical analyses and minimizing the probability of misidentifying
 the magnitude and direction of relationships between independent and
 dependent variables. In this study, we quantified song complexity for 367
 species of globally distributed songbirds (Passeriformes, Passeri). We
 quantified eight individual acoustic variables that have previously been
 linked to audio complexity which we analyzed independently, and after
 applying multivariate statistics to the variables. We used Bayesian linear
 mixed effect models to test multiple hypotheses regarding song complexity:
 that it should be greater in open habitats, in migratory species, for
 sexually monomorphic species, at higher latitudes and altitudes, and that
 it should co‐vary with clutch size characteristics. Our results challenge
 perceptions of the effect of habitat structure on song complexity; for
 instance, counter to expectation, we found songs in closed environments to
 have reduced syllable diversity. Additionally, our results suggest song
 complexity may not be ubiquitously a means of communicating male quality,
 with no significant difference between recordings from monomorphic and
 dimorphic species. By estimating song complexity in multiple ways, and
 quantifying these over large taxonomic and spatial scales, we are able to
 gain a more nuanced understanding of how song complexity is potentially
 affected by a range of biotic and abiotic factors. Our results also
 suggest that caution is required when making generalized statements about
 the relative influence of different factors on song complexity; more
 densely‐sampled, group‐specific studies are necessary complements to this
 taxonomically broad analysis.
description: songAnalysisAn R file showing how the analyses from the study were performedSongComplexityDataThe raw data for the study.
DOI: 10.5061/dryad.qk85bp8
title: Data from: Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna

description: Applications of DNA barcoding include identifying species, inferring
 ecological and evolutionary relationships between species, and DNA
 metabarcoding. These applications require reference libraries that are not
 yet available for many taxa and geographic regions. We collected,
 identified, and vouchered plant specimens from Mpala Research Center in
 Laikipia, Kenya, to develop an extensive DNA-barcode library for a savanna
 ecosystem in equatorial East Africa. We amassed up to five DNA barcode
 markers (rbcL, matK, trnL-F, trnH–psbA, and ITS) for 1,781 specimens
 representing up to 460 species (~92% of the known flora), increasing the
 number of plant DNA barcode records for Africa by ~9%. We evaluated the
 ability of these markers, singly and in combination, to delimit species by
 calculating intra- and inter-specific genetic distances. We further
 estimated a plant community phylogeny and demonstrated its utility by
 testing if evolutionary relatedness could predict the tendency of members
 of the Mpala plant community to have or lack “barcode gaps”, defined as
 disparities between the maximum intra- and minimum inter-specific genetic
 distances. We found barcode gaps for 72–89% of taxa depending on the
 marker or markers used. With the exception of the markers rbcL and ITS, we
 found that evolutionary relatedness was an important predictor of
 barcode-gap presence or absence for all of the markers in combination and
 for matK, trnL-F, and trnH–psbA individually. This plant DNA barcode
 library and community phylogeny will be a valuable resource for future
 investigations.
description: AlignmentsPhylogenyfinal.newR CodeGill et al MER Script.RmdBOLD Record DownloadsBOLD Downloads.zipBOLD MetadataMetadata for specimens included in version of record.bold.xlsx