cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bh126c0
title: Data from: GPS tracking and population genomics suggest itinerant breeding across drastically different habitats in the Phainopepla

description: Migratory birds generally divide the annual cycle between discrete
 breeding and non-breeding ranges. Itinerant breeders, however, reproduce
 twice at different geographic locations, migrating between them. This
 unusual flexibility in movement ecology and breeding biology suggests that
 some species can rapidly modulate the conflicting physiological and
 behavioral traits required for migration and reproduction. The Phainopepla
 (Phainopepla nitens), a songbird of the southwestern USA, has long been
 suspected to breed first in desert habitats in spring, then migrate to
 woodland habitats to breed again in summer. However, direct evaluation of
 movement and gene flow among individuals breeding in different locations
 has previously been logistically intractable. We deployed GPS tags on
 free-flying Phainopeplas in southern California, all of which migrated to
 hypothesized woodland breeding habitats after desert breeding (an average
 distance of 232 km). GPS data also revealed previously unknown fall and
 spring stopover sites. Population genomic analyses revealed no genetic
 differentiation among desert and woodland breeding populations, indicating
 significant movement and gene flow across the region. Finally, we used
 random forest analyses to quantify substantial environmental differences
 among temporal stages. Our results provide direct evidence that individual
 Phainopeplas do indeed move between two drastically different breeding
 habitats in the same year, representing a rare and extreme example of
 life-history flexibility.
description: Environmental
 DataClimate and NDVI data
 used in random forest analyses.GPS
 DataRaw data from five GPS
 tags.Dummy
 fileGenomic data used in
 phylogeographic analyses. See README file for details.Genomic_Data.tar
DOI: 10.5061/dryad.464pj40
title: Data from: Varying weed densities alters the corn transcriptome, highlighting a core set of weed-induced genes and processes with potential for manipulating weed tolerance

description: [No abstract provided]
description: supplemental table
 3
DOI: 10.5061/dryad.qm6530b
title: Data from: The way wear goes – phytolith-based wear on the dentine-enamel system in guinea pigs (Cavia porcellus)

description: The effect of phytoliths on tooth wear and function has been contested in
 studies of animal plant interactions. For herbivores whose occlusal
 chewing surface consists of enamel ridges in dentine tissue, the
 phytoliths might first erode the softer dentine, exposing the enamel
 ridges to different occlusal forces and thus leading to enamel wear. To
 test this hypothesis, we fed guinea pigs (Cavia porcellus; n=36 in 6
 groups) for three weeks exclusively on dry or fresh forage of low
 (lucerne), moderate (fresh timothy grass) or very high (bamboo leaves)
 silica content representing corresponding levels of phytoliths. We
 quantified the effect of these treatments with measurements from micro CT
 scans. Tooth height indicated extreme wear of the bamboo diet that
 apparently brought maxillary incisors and molars close to the minimum
 required for functionality. There were negative relationships between a
 cheek tooth’s height and the depth of its dentine basin, corroborating the
 hypothesis that dentine erosion plays an important role in herbivore tooth
 wear. In spite of lower body mass, bamboo-fed animals had paradoxically
 longer cheek tooth rows, and larger occlusal surfaces. Because
 ever-growing teeth can only change in shape from the base upwards, this is
 a strong indication that failure to compensate for wear by dental
 height-growth additionally triggered general expansive growth of the tooth
 bases. The results suggest that enamel wear may occur in sequence after
 dentine wear and not the other way around, and illustrate a surprising
 plasticity in the reactivity of this rodent’s system that adjusts tooth
 growth to wear.
description: mCT measurements of
 guinea pigs on different foragesMeasurements of
 morphometric skull parameters and dental measurements performed on DICOM
 stacks in Horos v3.3.3 with original data from mCT
 studies.LFM_GP_stats_190816.xlsx
DOI: 10.5061/dryad.b6vm63k
title: Data from: New and Old World phylogeography of pumpkinseed (Lepomis gibbosus): the North American origin of introduced populations in Europe

description: To determine the origin of introduced European populations of pumpkinseed
 (Lepomis gibbosus) – a freshwater sunfish, native to eastern North America
 that has spread across western and central Europe – we investigated the
 phylogeography of the species by sequencing the mitochondrial NADH subunit
 1 gene. A total of 543 pumpkinseed were sampled from 32 sites across the
 native range of the species, and from 19 sites covering much of its
 introduced European range. The presence and geographic distribution of two
 distinct clades in North American populations were discovered, suggesting
 that pumpkinseed survived the Pleistocene glaciations in two refugia
 (Atlantic and Mississippian). Analyses of mitochondrial variation revealed
 that European pumpkinseed may have been introduced to Europe from at least
 two distinct sources, but from the Atlantic drainages of North America
 only, which is consistent with historical records. Within Europe,
 haplotype distributions of pumpkinseed lend support to the entry of
 non-native fishes into Iberia via the so-called ‘Perpignan–Barcelona
 corridor’. European populations possessed lower genetic diversity than
 populations from North America, suggesting that low genetic diversity may
 not preclude a species from establishing and spreading into new
 environments outside of their native range.
description: Yavno_et_al_Hydrobiologia_HYDR-D-19-00318R1_Dryad_submission_dataExcel file: first worksheet lists sampling locations (including country and site names, latitude, longitude, sample size, and number of haplotypes); second worksheet is a matrix of haplotype occurrences (number of individuals with each haplotype) by population, using site codes listed in the first worksheet
DOI: 10.5061/dryad.tm06n0p
title: Data from: Rapid induction of the heat hardening response in an Arctic insect

description: The ability to cope with increasing and more variable temperatures, due to
 predicted climate changes, through plastic and/or evolutionary responses
 will be crucial for the persistence of Arctic species. Here, we
 investigate plasticity of heat tolerance of the Greenlandic seed bug
 Nysius groenlandicus, which inhabits areas with widely fluctuating
 temperatures. We test the heat resistance and hardening capacity
 (plasticity) of N. groenlandicus using both static (heat knock down time,
 HKDT) and dynamic (critical thermal maximum, CTmax) assays. We find that
 N. groenlandicus is able to tolerate short-term exposure to temperatures
 up to almost 50°C and that it can quickly increase heat resistance
 following heat hardening. Further, we find that this hardening response is
 reversible within hours after hardening. These findings contrast with
 common observations from temperate and tropical insects and suggest that
 more attention should be given to species in extreme and thermally
 variable environments such as Arctic and subarctic regions.
description: Hardening during
 temperature ramping (Figure 1) Heat hardening and
 recovery time (Figure 2a) Thermal exposure time
 (Figure 2b) Figure S2 (Heat
 hardening and recovery time) Supplementary
 data   
 Figure S3 (Heat
 hardening and recovery time) Supplementary
 data
DOI: 10.5061/dryad.n5j2h8d
title: Data from: Mechanisms for the development of microform patterns in peatlands of the Hudson Bay Lowland

description: Spatial surface patterns of hummocks, hollows, ridges, and pools
 (microtopography) are common features of many northern peatlands and are
 particularly distinct within the vast peatlands of the Hudson Bay Lowland
 (HBL), Canada. Hypotheses and models describe how small-scale feedbacks
 among vegetation, hydrology, and nutrients cause spatial differences in
 peat accumulation that enable microforms and surface patterns to develop
 over time. Empirical tests of the predictions from theoretical models of
 these proposed feedback mechanisms are limited, particularly in large
 peatland complexes such as the HBL. We investigate feedbacks controlling
 peatland structure and function in an ombrogenous bog and a minerogenous
 fen in the HBL. Our sites represent surface patterns found in many
 northern peatlands, specifically spatially irregular hummocks and hollows,
 and parallel ridges and pools that are perpendicular to slope. We found
 the occurrence of different spatial patterns depends on position within a
 peat landform, with these differences attributed to the ecohydrological
 setting. In turn, the ecohydrological setting, with different water table
 depths, nutrient availability, and species composition, influences the
 strength and direction of feedback mechanisms at the microform scale. Our
 data support the prediction of a positive feedback between plant
 productivity and acrotelm thickness for peat accumulation and hummock
 growth, and that this may be enhanced by water ponding on slopes to form
 ridge-pool tracks. We did not find evidence to support the proposed
 feedback among evapotranspiration (ET)-driven transport of water and
 nutrients for the development of hummocks. Our results suggest a
 combination of mechanisms operating at various temporal and spatial scales
 are associated with the development of surface patterns in northern
 peatlands.
description: CO2flux_MOECO2flux_MOE.csv – contains all carbon dioxide (CO2) fluxes (net ecosystem CO2 exchange, NEE, µmol m-2 s-1) measured at MOE Bog and MOE Fen with corresponding PPFD (photosynthetic photon flux density, µmol m-2 s-1).Vegetation_MOEVegetation_MOE.csv – contains percentage cover for species measured in 133 quadrats at MOE Bog and MOE Fen.NutrientsPRS_MOENutrientsPRS_MOE.csv – contains nutrient supply rates (µg 10 cm-2 week) for all plots at MOE Bog and MOE Fen. Measured using Plant Root Simulator (PRS) ion-exchange resin probes (PRSTM, Western Ag Innovation, Saskatoon, Saskatchewan, Canada).Elevation_MOEElevation_MOE.csv – contains surface elevation (m a.s.l.) of various microforms across MOE Bog and MOE Fen (measured in summer 2014).
DOI: 10.5061/dryad.n7kp793
title: Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing

description: Studies of structural variation (SV) have been challenging due to
 technological contraints. With the advent of third generation (long-read)
 sequencing technology, exploration of longer stretches of DNA not easily
 examined previously has been made possible. In the present study, we
 utilized third generation (long-read) sequencing techniques to examime SV
 in the EGFR landscape of four haplotypes derived from two human samples.
 We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using
 this sequencing approach and were able to identify regions of non-coding
 DNA which had relatively high similarity to the most common activating
 EGFR mutation in non-small cell lung cancer. We discovered that reverse
 complements to the exon 19 deletion mutation which had at least 60%
 homology to the EGFR exon 19 canonical deletion and were within ± 421,000
 bp of the deletion varied across the five haploid genomes examined (4
 patient landscapes and hg38). Although the sample size is limited in this
 study, the estimated variation observed in genomic stability between the
 five EGFR haplotypes examined is novel and encourages further work to
 examine structural variation in larger cohorts.
description: <strong>EGFR.4C.phase.0.consensus</strong><br>
 FASTA sequence file of the EGFR landscape of patient 4C
 <strong>EGFR.4C.phase.1.consensus</strong><br>
 FASTA sequence file of the EGFR landscape of patient 4C.
 <strong>EGFR.6C.phase.0.consensus</strong><br>
 FASTA sequence file of the EGFR landscape of patient 6C.
 <strong>EGFR.6C.phase.1.consensus</strong><br>
 FASTA sequence file of the EGFR landscape of patient 6C.
description: Targeted capture of long DNA fragments were obtained from each
 sample and submitted for long-read sequencing (Pacific Biosciences,
 SMRT<sup>®</sup> Sequencing with Sequel Binding Kit 2.0,
 Sequel Sequencing Plate 2.1). After primary analysis,
 Circular Consensus Sequence (CCS) reads were generated using SMRT Analysis
 6.0.0 for each dataset and aligned to the GRCh38 reference genome using
 minimap2. PCR duplicates from post-capture amplification were identified
 by mapping endpoints and tagged using a custom script (https://github.com/williamrowell/markdup). Short variants were joint-called using GATK4 HaplotypeCaller and filtered by quality metrics (SNPs and &gt;1bp indels, remove variants with QD&lt;2; 1bp indels, remove variants with QD&lt;5). The SNP sites that passed filtration were used in conjunction with the deduplicated CCS alignments for read-backed phasing with WhatsHap. We generated consensus sequences by applying phased SNP information to the reference FastA sequence using the VCFtools package. For each sample, the analysis results in regions with phased DNA haplotype landscapes (“haplotype separated”) separated by regions with one DNA landscape where the variants cannot be phased (“collapsed”).
DOI: 10.5061/dryad.0m76c00
title: Data from: Prevalence and abundance of bees visiting major conventionally-managed agricultural crops in Brazil

description: This study brings together data from a series of local pollinator surveys
 undertaken in major conventionally-managed agricultural crops in Brazil to
 determine the presence and abundance of bees visiting flowers within crops
 compared with adjacent off-crop habitats. Surveys were undertaken within
 crops and in adjacent off-crop areas using broadly the same methodology in
 flowering soybean, drybean, maize, citrus, coffee, rice, and cotton and in
 sugarcane immediately harvest. The bee species present were assessed twice
 per day at three times during crop flowering (post-harvest for
 sugar-cane). Pan traps were used to collect species present within the
 crop and off-crop twice per day. Drybeans, citrus, and coffee flowers
 displayed a consistent medium to high abundance of honey bees based on
 effort-adjusted transect and spot counts. In contrast, fields with
 flowering soybeans and cotton showed in-crop lower abundance and rice,
 corn, and harvested sugar cane showed consistently low numbers or no honey
 bees. In almost all cases honey bees were the most prevalent and abundant
 flower visitors within the studied crops. Where non-Apis bees were
 observed they often belong to the Meliponini (primarily Trigona) or the
 genera Bombus or Xylocopa. The off-crop assessments of species presence
 using pan traps showed a far wider diversity of species with greater
 proportional representation of solitary bee species. Overall, whilst honey
 bees accounted for the majority of observed bees visiting flowers in the
 agricultural fields, the off-crop habitat contained a greater abundance
 and diversity of non-Apis bee populations.
description: Brazil pollinator crop
 dataExcel data files for
 in-field surveys and off-crop surveys by transect, spot counts and
 pan-traps for soybean, coffee, citrus, sugarcane, drybean, rice, corn,
 cottonpollinator crop
 data.zip
DOI: 10.5061/dryad.6ft55k9
title: Data from: Evaluating presence-only species distribution models with discrimination accuracy is uninformative for many applications

description: Aim: Species distribution models are used across evolution, ecology,
 conservation, and epidemiology to make critical decisions and study
 biological phenomena, often in cases where experimental approaches are
 intractable. Choices regarding optimal models, methods, and data are
 typically made based on discrimination accuracy: a model’s ability to
 predict subsets of species occurrence data that were withheld during model
 construction. However, empirical applications of these models often
 involve making biological inferences based on continuous estimates of
 relative habitat suitability as a function of environmental predictor
 variables. We term the reliability of these biological inferences
 “functional accuracy.” We explore the link between discrimination accuracy
 and functional accuracy. Methods: Using a simulation approach we
 investigate whether models that make good predictions of species
 distributions correctly infer the underlying relationship between
 environmental predictors and the suitability of habitat. Results: We
 demonstrate that discrimination accuracy is only informative when models
 are simple and similar in structure to the true niche, or when data
 partitioning is geographically structured. However, the utility of
 discrimination accuracy for selecting models with high functional accuracy
 was low in all cases. Main conclusions: These results suggest that many
 empirical studies and decisions are based on criteria that are unrelated
 to models’ usefulness for their intended purpose. We argue that empirical
 modeling studies need to place significantly more emphasis on biological
 insight into the plausibility of models, and that the current approach of
 maximizing discrimination accuracy at the expense of other considerations
 is detrimental to both the empirical and methodological literature in this
 active field. Finally, we argue that future development of the field must
 include an increased emphasis on simulation; methodological studies based
 on ability to predict withheld occurrence data may be largely
 uninformative about best practices for applications where interpretation
 of models relies on estimating ecological processes, and will unduly
 penalize more biologically informative modeling approaches.
description: Simulation code for
 Warren et al. 2019 - Journal of BiogeographySimulation code to
 accompany Warren et al. 2019, examining the relationship between
 discrimination accuracy and functional accuracy for ENM/SDM
 studiessim-code-Warren-et-al-2019-master.zip
DOI: 10.5061/dryad.h19t7b2
title: Phylogenetic and Spatial Distribution of Evolutionary Isolation and Threat in Turtles and Crocodilians (Non-Avian Archosauromorphs)

description: The origin of turtles and crocodiles and their easily recognized body
 forms dates to the Triassic. Despite their long-term success, extant
 species diversity is low, and endangerment is extremely high compared to
 other terrestrial vertebrate groups, with ~ 65% of ~25 crocodilian and
 ~360 turtle species now threatened by exploitation and habitat loss. Here,
 we combine available molecular and morphological evidence with machine
 learning algorithms to present a phylogenetically-informed, comprehensive
 assessment of diversification, threat status, and evolutionary
 distinctiveness of all extant species. In contrast to other terrestrial
 vertebrates and their own diversity in the fossil record, extant turtles
 and crocodilians have not experienced any mass extinctions or shifts in
 diversification rate, or any significant jumps in rates of body-size
 evolution over time. We predict threat for 114 as-yet unassessed or
 data-deficient species and identify a concentration of threatened
 crocodile and turtle species in South and Southeast Asia, western Africa,
 and the eastern Amazon. We find that unlike other terrestrial vertebrate
 groups, extinction risk increases with evolutionary distinctiveness: a
 disproportionate amount of phylogenetic diversity is concentrated in
 evolutionarily isolated, at-risk taxa, particularly those with small
 geographic ranges. Our findings highlight the important role of geographic
 determinants of extinction risk, particularly those resulting from
 anthropogenic habitat-disturbance, which affect species across body sizes
 and ecologies.
description: archosauromorpha_Data_SourcesExcel file of all data sources and referencesarchosauromorpha_GenbankGenbank accession numbers for all sequence dataarchosauromorpha_ML_PhylogenyML phylogeny from RAxML in PDF format for viewingarchosauromorpha_ML_PhylogenyML phylogeny from RAxML in Newick format for analysisarchosauromorpha_PASTIS_386_10000Posterior distribution of 10,000 dated, taxonomically-complete phylogenies for non-avian Archosauromorpha, in Newick formatarchosauromorpha_PASTIS_386MrBayes input file for analyis, generated by PASTISarchosauromorpha_Spatial_Distance_MatrixSpatial-distance matrix of range centroids from all turtle and crocodilian speciesarchosauromorphaPartition file for RAxML analysis of phylogenyarchosauromorphaMatrix of DNA-sequence data in PHYLIP format for RAxML analysis
DOI: 10.5061/dryad.j18jt4n
title: Data from: Communities at the extreme: aquatic food webs in desert landscapes

description: Studying food webs across contrasting abiotic conditions is an important
 tool in understanding how environmental variability impacts community
 structure and ecosystem dynamics. The study of extreme environments
 provides insight into community-wide level responses to environmental
 pressures with relevance to the future management of aquatic ecosystems.
 In the western Lake Eyre Basin of arid Australia, there are two
 characteristic and contrasting aquatic habitats: springs and rivers.
 Permanent isolated Great Artesian Basin springs represent hydrologically
 persistent environments in an arid desert landscape. In contrast,
 hydrologically variable river waterholes are ephemeral in space and time.
 We comprehensively sampled aquatic assemblages in contrasting ecosystem
 types to assess patterns in community composition and to quantify food web
 attributes with stable isotopes. Springs and rivers were found to have
 markedly different invertebrate communities, with rivers dominated by more
 dispersive species and springs associated with species that show high
 local endemism. Qualitative assessment of basal resources shows
 autochthonous carbon appears be a key basal resource in both types of
 habitat, although the particular sources differed between habitats.
 Food-web variables such as trophic length, trophic breadth and community
 isotopic niche size were relatively similar in the two habitat types. The
 basis for the similarity in food-web structure despite differences in
 community composition appears to be broader isotopic niches for predatory
 invertebrates and fish in springs as compared with rivers. In contrast to
 published theory, our findings suggest that the food webs of the
 hydrologically variable river sites may show less dietary generalisation
 and more compact food-web modules than in springs.
description: Data_Aquatic food webs
 in desert landscapesSheet 1.
 "SiteData", locations and site ID codes for study sites; Sheet
 2. “StableIsotopeData_All”, all fauna and flora sample SIA data; Sheet 3.
 “InvertSampling_Presense-Absence”, presence (1) and absence (0) of
 invertebrate taxa by sample.Data_Aquaticfoodwebsindesertlandscapes_dryad.xlsx