cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s156b
title: Data from: Quantifying and modelling decay in forecast proficiency indicates the limits of transferability in land-cover classification

description: 1. The ability to provide reliable projections for the current and future
 distribution patterns of land-covers is fundamental if we wish to protect
 and manage our diminishing natural resources. Two inter-related
 revolutions made map productions feasible at unprecedented resolutions-
 the availability of high-resolution remotely-sensed data and the
 development of machine-learning algorithms. However, the ground-truth data
 needed for training models is in most cases spatially and temporally
 clustered. Therefore, map production requires extrapolation of models from
 one place to another and the uncertainty cost of such extrapolation is
 rarely explored. In other words, we focus mainly on projections, and less
 on quantifying how reliable they are. 2. Following the concept of
 ‘forecast horizon’, we suggest that the predictability of land-cover
 classification models should be methodologically explored with
 quantitative tools as a continuum against distances measured along
 multiple dimensions. Focusing on ten agricultural sites from England and
 using models specifically designed to predict multivariate decay-curves we
 ask: how does a model’s predictive performance decay with distance? More
 specifically, we explored if we could predict the proficiency (kappa
 statistics) of a model trained in one site when making predictions in
 another site based on the spatial, temporal, spectral and environmental
 distances between sites. 3. We found that model proficiency decays with
 spatial, temporal, spectral and environmental distance between sites. More
 importantly, we found for the first time that it is possible to predict
 the performance a model transferred to or from a novel site will have,
 based on its distances from known sites. The spatial distance variables
 where the most important when predicting model transferability. 4.
 Exploring model transferability as a continuum may have multiple usages
 including predicting uncertainty values in space and time, prioritization
 of strategies for ground-truth data collection, and optimizing model
 characteristics for defined tasks.
description: GavishEtAl2017Dryad
DOI: 10.5061/dryad.c0765
title: Data from: Hovering in the heat: effects of environmental temperature on heat regulation in foraging hummingbirds

description: At high temperature (&gt;40 ºC) endotherms experience reduced passive
 heat dissipation (radiation, conduction, and convection) and increased
 reliance on evaporative heat loss. High temperatures challenge flying
 birds due to heat produced by wing muscles. Hummingbirds depend on flight
 for foraging, yet inhabit hot regions. We used infrared thermography to
 explore how lower passive heat dissipation during flight impacts body-heat
 management in broad-billed (Cynanthus latirostris, 3.0g), black-chinned
 (Archilochus alexandri, 3.0g), Rivoli’s (Eugenes fulgens, 7.5g), and
 blue-throated (Lampornis clemenciae, 8.0g) hummingbirds in southeastern
 Arizona and calliope hummingbirds (Selasphorus calliope, 2.6 g) in
 Montana. Thermal gradients driving passive heat dissipation through eye,
 shoulder and feet dissipation areas are eliminated between 36-40 ºC.
 Thermal gradients persisted at higher temperatures in smaller species,
 possibly allowing them to inhabit warmer sites. All species experienced
 extended daytime periods lacking thermal gradients. Broad-billed
 hummingbirds lacking thermal gradients regulated mean total-body surface
 temperature at ~38 ºC suggesting behavioral thermoregulation.
 Blue-throated hummingbirds were inactive when lacking passive heat
 dissipation, so might have the lowest temperature tolerance of the four
 species. Use of thermal refugia permitted hummingbirds to tolerate higher
 temperatures, but climate change could eliminate refugia, forcing
 distributional shifts in hummingbird populations.
description: El Coronado Site
 Temperature DataContains the all
 individual measurements from all temperature sensors at the El Coronado
 Study site.EC
 Temperature.xlsxSouthwestern Research
 Station Site Temperature DataContains the all
 individual measurements from all temperature sensors at the Southwestern
 Research Station study site.SWRS
 Temperature.xlsxHarshaw Creek Site
 Temperature DataContains the all
 individual measurements from all temperature sensors at the Harshaw Creek
 study site.HC
 Temperature.xlsxSonoita Creek Site
 Temperature DataContains the all
 individual measurements from all temperature sensors at the Sonoita Creek
 study site.SC
 Temperature.xlsxHead Transect IR
 DataRaw data from our
 analysis of hummingbird head transects from infrared
 images.Head
 Transect Data.xlsxHummingbird Ts verses Te
 Comparison DataIndividual measurements
 of whole-body surface temperature and corresponding environmental
 temperature used to analyzed patterns of whole-body surface temperature
 change across the range of environmental temperatures measured in this
 study.Ts vs
 Te Data.xlsxEffect of Environmental
 Temperature on Body vs HDAIndividual measurements
 of whole-body surface temperature and corresponding environmental
 temperature used to analyzed environmental impact on whole-body surface
 temperature and heat dissipation area surface
 temperature.Figure 2
 Data.xlsx
DOI: 10.5061/dryad.fd57r
title: Data from: Using soil amendments and plant functional traits to select native tropical dry forest species for the restoration of degraded Vertisols

description: Tropical dry forests (TDFs) are critically endangered, and their
 restoration is understudied. Large-scale passive restoration efforts in
 north-west (NW) Costa Rica have catalysed TDF regeneration but are not
 effective on degraded Vertisols, where active restoration is necessary due
 to high content of shrink–swell clays that impede regeneration following
 degradation. We established a large-scale restoration experiment in
 degraded former pastures in NW Costa Rica to determine (1) the restoration
 potential of native TDF tree species on Vertisols, (2) if plant functional
 traits elucidate mechanisms behind interspecific variability in species
 performance and (3) if affordable and readily available soil amendments
 increase seedling survivorship and growth. We planted 1,710 seedlings of
 32 native species coupled with five amendments aimed at ameliorating
 root-zone microclimatic conditions: sand, rice hulls, rice hull ash,
 hydrogel and unamended controls. For each species, we quantified a suite
 of resource-acquisition and ecophysiological functional traits, and
 monitored survival and growth seasonally over 2 years. Interspecific
 survivorship after 2 years ranged widely (0%–92.5%). Functional traits
 including wood density, photosynthetic parameters and upregulation of
 integrated water-use efficiency, explained interspecific variation in
 survivorship and growth at distinct ontogenetic stages. Easily measured
 leaf traits, however, were not good predictors of restoration potential.
 Hydrogel and sand amendments increased initial seedling survival, but
 after 2 years no differences among treatments were found. Synthesis and
 applications. We have shown it is possible, albeit challenging, to restore
 tropical dry forest (TDF) on degraded Vertisols. Our results support the
 use of functional trait-based screenings to select tree species for
 restoration projects as tree species with high survivorship and growth in
 this stressful environment have overlapping ecophysiological functional
 traits. Furthermore, practitioners should consider water-use and
 phytosynthetic traits when designing initial species mixes for TDF
 restorations.
description: Species-level functional
 trait values for 32 tropical dry forest tree speciesspecies_level_traits_Werden_et_al.csvSurvival and growth surveys for 32 tropical dry forest tree species in a restoration experiment on degraded Vertisolssurvival_growth_surveys_Werden_et_al.csv
DOI: 10.5061/dryad.8d0h5
title: Data from: A load-based mechanism for inter-leg coordination in insects

description: Animals rely on an adaptive coordination of legs during walking. However,
 which specific mechanisms underlie coordination during natural locomotion
 remains largely unknown. One hypothesis is that legs can be coordinated
 mechanically based on a transfer of body load from one leg to another. To
 test this hypothesis, we simultaneously recorded leg kinematics, ground
 reaction forces and muscle activity in freely walking stick insects
 (Carausius morosus). Based on torque calculations, we show that load
 sensors (campaniform sensilla) at the proximal leg joints are well suited
 to encode the unloading of the leg in individual steps. The unloading
 coincides with a switch from stance to swing muscle activity, consistent
 with a load reflex promoting the stance-to-swing transition. Moreover, a
 mechanical simulation reveals that the unloading can be ascribed to the
 loading of a specific neighbouring leg, making it exploitable for
 inter-leg coordination. We propose that mechanically mediated load-based
 coordination is used across insects analogously to mammals.
description: Supporting data for
 figure 2Torques and torque rates
 at the CTr joint of right middle legs during stance. Data are normalized
 to stance duration. n_animal indicates animal number. n_step indicates
 step number per animal. percent_stance indicates the percent of the stance
 phase. Torque is given in µNm. Torque rate is given in
 µNm/s.data_figure_2.txtSupporting data for figure 3Times of levator and depressor muscle activity, time of leg unloading and joint angles of right middle legs during stance. Data are normalized to stance duration. n_step indicates step number. percent_stance indicates the percent of the stance phase. levator_activity = 1 or depressor_activity = 1 indicates that the respective muscle was active at the given time of the stance phase. tUL = 1 indicates the onset of leg unloading. Joint angles are given in degree.data_figure_3.txtSupporting data for figure 4Touch-downs of legs relative to the onset of unloading in the right middle leg and their simulated unloading efficacy. n_step indicates step number. Times of touch-downs are given in ms. Efficacy is given in µNm (middle leg CTr torque). Each leg is labeled as being a right (R) or left (L) and a front (F), middle (M) or hind (H) leg. Note that we excluded the touch-down of a leg from efficacy calculations if it occurred simultaneously with the touch-down or lift-off of another leg. In this case, the change in middle leg CTr torque could not be ascribed to the action of any one leg alone.data_figure_4.txt
DOI: 10.5061/dryad.53jb9
title: Data from: Morphological integration in the appendicular skeleton of two domestic taxa: the horse and donkey

description: Organisms are organized into suites of anatomical structures that
 typically covary when developmentally or functionally related, and this
 morphological integration plays a determinant role in evolutionary
 processes. Artificial selection on domestic species causes strong
 morphological changes over short time spans, frequently resulting in a
 wide and exaggerated phenotypic diversity. This raises the question of
 whether integration constrains the morphological diversification of
 domestic species and how natural and artificial selection may impact
 integration patterns. Here, we study the morphological integration in the
 appendicular skeleton of domestic horses and donkeys, using
 three-dimensional geometric morphometrics on 75 skeletons. Our results
 indicate that a strong integration is inherited from developmental
 mechanisms which interact with functional factors. This strong integration
 reveals a specialization in the locomotion of domestic equids, partly for
 running abilities. We show that the integration is stronger in horses than
 in donkeys, probably because of a greater degree of specialization and
 predictability of their locomotion. Thus, the constraints imposed by
 integration are weak enough to allow important morphological changes and
 the phenotypic diversification of domestic species.
description: Hanot_et_al_PC_scoresPC scores used in the shape covariation analyses. In capital letters: the couple in which the concerned bone (in lower case) is included (scap : scapula ; hum : humerus ; rad : radius-ulna ; mtc : metacarpal bone ; pa1 : proximal anterior phalanx ; pa2 : middle anterior phalanx ; pa3 : distal anterior phalanx ; cox: coxal bone; fem: femur; tib: tibia; tal: talus; cal: calcaneus; mtt: metatarsal bone; pp1 : proximal posterior phalanx ; pp2 : middle posterior phalanx ; pp3 : distal posterior phalanx)
DOI: 10.5061/dryad.j6q05
title: Data from: Interacting effects of unobserved heterogeneity and individual stochasticity in the life-history of the Southern fulmar

description: 1.Individuals are heterogeneous in many ways. Some of these differences
 are incorporated as individual states (e.g., age, size, breeding status)
 in population models. However, substantial amounts of heterogeneity may
 remain unaccounted for, due to unmeasurable genetic, maternal, or
 environmental factors. 2.Such unobserved heterogeneity (UH) affects the
 behavior of heterogeneous cohorts via intra-cohort selection and
 contributes to inter-individual variance in demographic outcomes such as
 longevity and lifetime reproduction. Variance is also produced by
 individual stochasticity, due to random events in the life cycle of wild
 organisms, yet no study thus far has attempted to decompose the variance
 in demographic outcomes into contributions from unobserved heterogeneity
 and individual stochasticity for an animal population in the wild. 3.We
 developed a stage-classified matrix population model for the Southern
 fulmar breeding on Ile des Pétrels, Antarctica. We applied multi-event,
 multi-state markrecapture methods to estimate a finite mixture model
 accounting for UH in all vital rates and Markov chain methods to calculate
 demographic outcomes. Finally, we partitioned the variance in demographic
 outcomes into contributions from unobserved heterogeneity and individual
 stochasticity. 4.We identify three UH groups, differing substantially in
 longevity, lifetime reproductive output, age at first reproduction, and in
 the proportion of the life spent in each reproductive state. 14% of
 individuals at fledging have a delayed but high probability of recruitment
 and extended reproductive lifespan. 67% of individuals are less likely to
 reach adulthood, recruit late and skip breeding often but have the highest
 adult survival rate. 19% of individuals recruit early and attempt to breed
 often. They are likely to raise their offspring successfully, but
 experience a relatively short lifespan. Unobserved heterogeneity only
 explains a small fraction of the variances in longevity (5.9%), age at
 first reproduction (3.7%) and lifetime reproduction (22%). 5.UH can affect
 the entire life cycle, including survival, development, and reproductive
 rates, with consequences over the lifetime of individuals and impacts on
 cohort dynamics. The respective role of unobserved heterogeneity versus
 individual stochasticity varies greatly among demographic outcomes. We
 discuss the implication of our finding for the gradient of life-history
 strategies observed among species and argue that individual differences
 should always be accounted for in demographic studies of wild populations.
description: Jenouvrier_et_al_2017_JAESee Supplementary material and section 7: Other data available on Dryad, for a detailed description of the files.
DOI: 10.5061/dryad.r35kr
title: Data from: Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping

description: Taro, Colocasia esculenta, is one of the world’s oldest root crops and of
 particular economic and cultural significance in Hawai‘i, where
 historically more than 150 different landraces were grown. We developed a
 genome-wide set of more than 2400 high-quality single nucleotide
 polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South
 Pacific, Palauan, and mainland Asian origins, with several objectives: (a)
 uncover the phylogenetic relationships between Hawaiian and other Pacific
 landraces, (b) shed light on the history of taro cultivation in Hawai‘i,
 and (c) develop a tool to discriminate among Hawaiian and other taros. We
 found that almost all existing Hawaiian landraces fall into five
 monophyletic groups that are largely consistent with the traditional
 Hawaiian classification based on morphological characters, e.g., leaf
 shape and petiole color. Genetic diversity was low within these clades but
 considerably higher between them. Population structure analyses further
 indicated that the diversification of taro in Hawai‘i most likely occurred
 by a combination of frequent somatic mutation and occasional
 hybridization. Unexpectedly, the South Pacific accessions were found
 nested within the clades mainly composed of Hawaiian accessions, rather
 than paraphyletic to them. This suggests that the origin of clades
 identified here preceded the colonization of Hawai‘i, and that early
 Polynesian settlers brought taro landraces from different clades with
 them. In the absence of a sequenced genome, this marker set provides a
 valuable resource towards obtaining a genetic linkage map, and to study
 the genetic basis of phenotypic traits of interest to taro breeding such
 as disease resistance.
description: HawaiianTaro_SNP.vcfZip archive of eight SNP datasets in VCF format, obtained by four SNP calling methods: GBS+RAD, GBS subset, transcriptome, and UNEAK (see Materials and methods). Each was filtered by minor allele count ≥ 2 (mac2) and minor allele frequency ≥ 0.1 (maf10). The primary dataset was based on GBS+RAD and mac2.HawaiianTaro_SNP.fasZIP archive of two SNP datasets used for phylogenetic analyses in FASTA format, homozygous positions only (nomenclature see VCF files).
DOI: 10.5061/dryad.b744g
title: Data from: Multi-jawed chaetognaths from the Chengjiang Lagerstätte (Cambrian, Series 2, Stage 3) of Yunnan, China

description: Chaetognaths (arrow-worms) are enigmatic in terms of their phylogenetic
 position, while the existence of Protosagitta spinosa from the Chengjiang
 Lagerstätte suggests minimal change in their unique bodyplan since at
 least the early Cambrian. Apart from rare (and sometimes controversial)
 soft-bodied remains, the fossil record of chaetognaths is otherwise almost
 entirely dependent on early Palaeozoic phosphatic microfossils, some of
 which are placed amongst so-called protoconodonts. Fused spine clusters
 are strikingly similar to the cephalic grasping apparatus of extant forms
 and are assumed to have had a comparable configuration. Here we report a
 new chaetognath, Ankalodous sericus gen. et sp. nov., coeval with
 Protosagitta but with a complex feeding apparatus consisting of multiple
 bundles of recurved spines whose principal function appears to have been
 grasping. Like all other chaetognaths a predatory mode of life is likely,
 but its position relative to the sediment–water interface is less certain.
 Reduction of the feeding apparatus, from the multi-jawed arrangement of A.
 sericus to the grasping spines and associated smaller teeth seen in other
 chaetognaths, was probably a subsequent development and conceivably was
 linked with a shift to a pelagic mode of life. We also report a new
 specimen of Protosagitta. This confirms earlier observations but it
 possesses hitherto unrecognized features, including a cephalic tentacle
 and fin rays.
description: Appendix
 S1Methods summary and
 character-taxon matrix used for cladistic analysis (nexus format). File
 readable using a text editor.Appendix
 S2Character-taxon matrix
 and settings used for cladistic analysis (BEAST 2 xml format). File
 readable using a text editor.AppendixS2.xmlAppendix S3Ankalodous sericus, ELI-Erjie-009; light microscopy (A) and back-scatter electron imagery (B, C). (A) Entire specimen, with box indicating field shown in (B). (B) Detail of grasping array, with box indicating field shown in (C). (C) Detail of spines, showing framboidal pyritic infills of internal cavities.AppendixS3.jpgAppendixS4Raman spectroscopy of five specimens of Ankalodous sericus, showing spectograms of spines (A-C, E), putative plate (D) in locations of yellow dots and adjacent sediment (E) in locations with white squares. Raman spectroscopy of the spines follows a two-peak model (respective values of 1382.12, 1611.68), consistent with the presence of organic carbon.
DOI: 10.5061/dryad.n1851
title: Data from: Different from trees, more than metaphors: branching silhouettes—corals, cacti, and the oaks

description: There has long been ambiguity in the use of the term tree in phylogenetic
 systematics, which is a continuous source of misinterpretation of
 evolutionary relationships. The basic problem is that while many trees
 with phylogenetic or evolutionary relevance, such as cladograms, are
 consistent with graph theory, tree-like visualization of phylogeny may
 also be done via other types of graphics, especially botanical (or
 literal) tree drawings. As a consequence, the meaning of such diagrams is
 not always clear: a given picture may have multiple interpretations in its
 different parts and two figures that look similar may actually carry quite
 different information. I show that these are not merely metaphors of
 phylogeny and may be defined mathematically as geometric shapes called
 branching silhouette diagrams, the name referring to their most apparent
 features. They have four basic forms depending on whether the time factor
 is considered in their construction and the relationships portrayed are of
 the ancestor–descendant or sister group type. By revitalizing Darwin’s
 early suggestions on the illustration of change in the living world, I
 propose the term coral for the most common forms of branching silhouette
 which consider time and show ancestry. The others appear rarely in
 present-day practice and are mostly of historical value—these are cacti
 (named after one of Bessey’s diagrams) and two types of oaks (with
 reference to several of Haeckel’s motifs used in depicting phylogeny in
 the nineteenth century). The use of these terms in phylogenetic
 systematics facilitates better understanding of how organization of
 biodiversity has been visualized in science.
description: Historical phylogenetic
 diagramsCoralAppendixR2.pdf
DOI: 10.5061/dryad.5sb71
title: Data from: Widespread introgression in Chinese indigenous chicken breeds from commercial broiler

description: Chinese indigenous chickens constitute world-renowned genetic resources
 due to their excellent traits, including early puberty, good meat quality,
 and strong resistance to disease. Unfortunately, the introduction of a
 large number of commercial chickens in the past two decades has had an
 adverse effect on Chinese indigenous chickens. Using the chicken 60K
 single-nucleotide polymorphism (SNP) chip, we assessed the genetic
 diversity and population structure of 1,187 chickens, representing eight
 Chinese indigenous chicken breeds, two hybrid chicken breeds, two
 ancestral chicken breeds, two commercial populations, and additional red
 jungle fowl. By investigating haplotype similarity, we found extensive
 gene introgression from commercial broiler to almost all Chinese
 indigenous chickens. Approximately 15% of the genome, on average, of
 Chinese indigenous chickens was introgressed, ranging from 0.64% for
 Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis
 revealed signals consistent with positive selection in the introgression
 loci. For the first time, we systematically mapped and quantified
 introgression from commercial broiler to Chinese indigenous chickens at
 the whole genome level. Our data provided a usable resource for chicken
 genetic diversity, and our findings indicated a dire need for protecting
 the genetic resources of Chinese indigenous chickens.
description: Chinese_indigenous_chickensGenotype data for chinese indigenous chickens