cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34tmpg4hd
title: Geographic patterns of genomic variation in the threatened Salado salamander, Eurycea chisholmensis

description: Aquatic, karst and spring endemic organisms have become a focus of
 conservation efforts as human population densities and demand for
 groundwater increase. This is especially true of Texas salamanders in the
 genus Eurycea that have been the subject of investigations of patterns of
 genetic differentiation in order to understand their systematics and to
 inform conservation planning. Here we quantify patterns of population
 differentiation in the northern most species, Eurycea chisholmensis, the
 Salado salamander, which is listed as a federally threatened species.
 Several thousand single nucleotide markers (SNPs) were used to quantify
 within- and among-population genetic variation. We used approximate
 Bayesian computation and a method based on linkage disequilibrium to
 estimate effective population size, Ne. Levels of differentiation were
 low, but revealed a primary division between northern and southern
 populations with no evidence of gene exchange between them. Pairwise
 differentiation, estimated as Gst, ranged from 0.0042 within regions to
 0.0244 between regions. Genetic diversity was similar across all sampling
 locations and estimates of Ne were largely congruent across two methods
 and indicate population sizes large enough to maintain genetic variation,
 at least over the short term. These results can inform ongoing
 conservation efforts for this threatened species.
description: Matrix of posterior genotype probabilities for 175 salamanders at
 8,731 SNP loci generated by genotyping-by-sequencing methods (similar to
 ddRAD.seq methods). The hierarchical Bayesian clustering algorithm ENTROPY
 was used to generate these genotype probabilities.
description: This genotype matrix contains no missing data and can be used as
 is. Two additional files conatining individual identifiers in order and
 another with a key to locality codes accompany the genotype data
 dile.
DOI: 10.5061/dryad.s1rn8pk5m
title: Phenotype pictures of Arabidopsis thaliana in high light and low light conditions

description: The rate at which plants grow is a major functional trait in plant
 ecology. However, little is known about its evolution in natural
 populations. Here, we investigate evolutionary and environmental factors
 shaping variation in the growth rate of Arabidopsis thaliana. We used
 plant diameter as a proxy to monitor plant growth over time in
 environments that mimicked latitudinal differences in the intensity of
 natural light radiation, across a set of 278 genotypes sampled within four
 broad regions, including an outgroup set of genotypes from China. The
 observed variation was validated in a field experiment conducted under
 natural conditions. All genotypes grew markedly wider rosettes when the
 light supply was decreased, demonstrating that environmental plasticity is
 a predominant source of variation to adapt plant size to prevailing light
 conditions. Yet, we detected significant levels of genetic variation both
 in growth rate and growth plasticity. Genome-wide association studies
 revealed that only 2 single nucleotide polymorphisms associate with
 genetic variation for growth above Bonferroni confidence levels. However,
 marginally associated variants were strongly enriched among genes with an
 annotated role in growth and stress reactions. Polygenic scores computed
 from marginally associated variants confirmed the polygenic basis of
 growth variation. For both light regimes, phenotypic divergence between
 Europe and the distantly related populations of China is smaller than the
 variation observed within Europe indicating that plant growth is
 constrained by stabilizing selection. We observed that Spanish genotypes,
 however, reach a significantly larger size than Northern European
 genotypes. Tests of adaptive divergence and analysis of the individual
 burden of deleterious mutations reveal that adaptive processes have played
 a more important role in shaping regional differences in rosette growth
 than maladaptive evolution.
description: The rows in the trays were rotated, so the position of a
 particular plant changes between dates.<br> Files with the position
 of each plant are supplied.<br> The plants had linenumbers assigned,
 which can be linked to the ID in the info file provided.<br> Trays
 1-8 are the first replicate/block, 9-16 the second and 17-24 the third
 replicate.
DOI: 10.5061/dryad.3ffbg79gb
title: Data from: Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype

description: Understanding the effect of human induced landscape fragmentation on gene
 flow and evolutionary potential of wild populations has become a major
 concern. Here, we investigated the effect of riverscape fragmentation on
 patterns of genetic diversity in the freshwater resident European brook
 lamprey (Lampetra planeri) that has a low ability to pass obstacles to
 migration. We also tested the hypotheses of i) asymmetric gene flow
 following water current and ii) a positive effect of admixture
 with the closely related anadromous river lamprey (L.
 fluviatilis) ecotype on L. planeri genetic diversity. We
 genotyped 2472 individuals, including 225 L. fluviatilis, sampled
 from 81 sites upstream and downstream barriers to migration, in
 29 western European rivers. Linear modelling revealed a strong positive
 relationship between genetic diversity and the
 distance from the river source, consistent with
 expected patterns of decreased gene flow into upstream populations.
 However, the presence of anthropogenic barriers had a moderate effect on
 spatial genetic structure. Accordingly, we found evidence for
 downstream-directed gene flow, supporting the hypothesis that barriers do
 not limit dispersal mediated by water flow. Downstream L. planeri
 populations in sympatry with L. fluviatilis displayed consistently higher
 genetic diversity. We conclude that genetic drift and slight downstream
 gene flow drive the genetic make-up of upstream L. planeri
 populations whereas admixture between ecotypes maintains higher
 levels of genetic diversity in L. planeri
 populations sympatric with L. fluviatilis. We discuss
 the implications of these results for the design of conservation
 strategies of lamprey, and other freshwater organisms with several
 ecotypes, in fragmented dendritic river networks.
DOI: 10.5061/dryad.cz8w9gj1w
title: Evolution of chain migration in an aerial insectivorous bird, the common swift Apus apus

description: Spectacular long-distance migration has evolved repeatedly in animals
 enabling exploration of resources separated in time and space. In birds,
 these patterns are largely driven by seasonality, cost of migration, and
 asymmetries in competition leading most often to leap-frog migration,
 where northern breeding populations winter furthest to the south. Here we
 show that the highly aerial common swift Apus apus, spending the
 non-breeding period on the wing, instead exhibits a rarely-found chain
 migration pattern, where the most southern breeding populations in Europe
 migrate to wintering areas furthest to the south in Africa, while the
 northern populations winter to the north. The swifts concentrated in three
 major areas in sub-Saharan Africa during the non-breeding period, with
 substantial overlap for nearby breeding populations. We found that the
 southern breeding swifts were larger, raised more young, and arrived to
 the wintering areas with higher seasonal variation in greenness
 (Normalized Difference Vegetation Index, NDVI) earlier than the northern
 breeding swifts. This unusual chain migration pattern in common swifts is
 largely driven by differential annual timing and we suggest it evolves by
 prior occupancy and dominance by size in the breeding quarters and by
 prior occupancy combined with diffuse competition in the winter.
description: Average winter position in November and December fo rindividually
 tracked common swifts (Apus apus) breeding in Europe. Tracking method
 geolocation by light.   Clutch size measured as maximum
 number of young in nest.  Wing and mass of common
 swifts breeding in Europe. Wing and mass collected during ringing at
 breeding sites.
DOI: 10.5061/dryad.jsxksn073
title: Data from: Quorum-sensing signaling by chironomid egg masses’ microbiota affects haemagglutinin/protease (HAP) production by Vibrio cholerae

description: Vibrio cholerae, the causative agent of cholera, is commonly isolated,
 along with other bacterial species, from chironomid insects (Diptera:
 Chironomide). Nevertheless, its prevalence in the chironomid egg masses’
 microbiota is less than 0.5%. V. cholerae secretes haemagglutinin/protease
 (HAP) that degrades the gelatinous matrix of chironomid egg masses and
 prevents hatching. Quorum sensing (QS) activates HAP production in
 response to accumulation of bacterial autoinducers (AIs). Our aim was to
 define the impact of chironomid microbiota on HAP production by V.
 cholerae. To study QS signaling, we used V. cholerae bioluminescence
 reporter strains (QS-proficient O1 El-Tor wild type and QS-deficient
 mutants) and different bacterial species that we isolated from chironomid
 egg masses. These egg mass isolates, as well as a synthetic AI-2, caused
 an enhancement in lux expression by a V. cholerae QS-deficient mutant. The
 addition of the egg mass bacterial isolate supernatant to the QS-deficient
 mutant also enhanced HAP production and egg mass degradation activities.
 Moreover, the V. cholerae wild type strain was able to proliferate using
 egg masses as their sole carbon source while the QS-deficient was not. The
 results demonstrate that members of the chironomid bacterial consortium
 produce external chemical cues that, like AI-2, induce expression of the
 hapA gene in V. cholerae. Understanding the interactions between V.
 cholerae and the insects’ microbiota may help uncover the interactions
 between this pathogen and the human gut microbiota.
DOI: 10.5061/dryad.51c59zw69
title: The functional significance of panting as a mechanism of thermoregulation and its relationship to the critical thermal maxima in lizards

description: Because most desert-dwelling lizards rely primarily on behavioral
 thermoregulation for the maintenance of active body temperatures, the
 effectiveness of panting as a thermoregulatory mechanism for evaporative
 cooling has not been widely explored. We measured changes in body
 temperature (Tb) with increasing air temperature (Ta) for seventeen
 species of lizards that range across New Mexico and Arizona and quantified
 the temperatures associated with the onset of panting, the capacity of
 individuals to depress Tb below Ta while panting and estimated the
 critical thermal maxima (CTmax) for each individual. We examined these
 variables as a function of phylogeny, body mass, and local acclimatization
 temperature. We found that many species can depress Tb 2-3°C below Ta
 while panting, and the capacity to do so appears to be a function of each
 species’ ecology and thermal environment, rather than phylogeny. Panting
 thresholds and CTmax’s are phylogenetically conserved within groups.
 Understanding the functional significance of panting and its potential
 importance as a thermoregulatory mechanism will improve our understanding
 of the potential for species’ persistence in an increasingly warmer world.
DOI: 10.5068/d10m4s
title: Van Allen Probes MagEIS sensor response functions

description: We provide the NASA Van Allen Probes MagEIS electron spectrometers’
 response function files and a detailed README document that details their
 format and use. The full 3D (energy-angle-angle) response files are
 provided in HDF5 format, along with 1D isotropic response function files
 in CSV format. The necessary lookup tables are also provided. 
 Details on the Geant4 simulations and the energy/angular response of the
 sensors are provided in the Space Science Reviews manuscript “The Magnetic
 Electron Ion Spectrometer: A Review of On-Orbit Sensor Performance, Data,
 Operations, and Science” by Claudepierre et al.
DOI: 10.15468/dl.vskhjv
title: Occurrence Download

description: A dataset containing 684 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((100 -62,99 -62,99 -63,100 -63,100 -62))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 684 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002549-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8h920
title: Mean flow direction modulates non-Fickian transport in a heterogeneous alluvial aquifer-aquitard system

description: Regional-scale groundwater quality degradation from nonpoint source
 pollution threatens the long-term sustainability of major alluvial
 aquifer-aquitard systems worldwide. Upscaled models can efficient
 represent nonpoint source transport, but fail to accurately characterize
 non-Fickian (anomalous) transport caused by mean flow direction
 transience. In this study, we demonstrate that hydrogeologic factors
 explain this failure. Specifically, vertical anisotropy in K and seasonal
 pumping and recharge in typical alluvial aquifer systems can fundamentally
 change hydraulic gradients and shift the mean flow direction between
 mostly horizontal and mostly vertical flow. Detailed 3D flow and transport
 simulations in a heterogeneous alluvial aquifer under varying mean flow
 directions indicate that alterations to hydraulic gradients which control
 the mean flow direction can lead to increasingly non-Fickian transport.
 Under mostly horizontal flow, diffusion and slow advection dominant low-K
 facies slow mass transfer rates from low-K material, and preferential flow
 along connected high-K networks causes increased spatial spreading along
 the mean flow direction. Conversely, predominantly vertical flow caused by
 spatially distributed pumping and recharge shifts mass transfer processes
 in low-K material from diffusion and slow advection dominant to advection
 dominant, which results in vertically oriented particle trajectories that
 compactly migrate through high- and low-K facies alike, leading to
 increasingly Fickian transport. Thus, mean flow direction transience
 driven by vertical anisotropy in K and seasonal pumping and recharge can
 create oscillating transport patterns, ranging from persistently
 non-Fickian to more Fickian. Results illustrate the hydrogeologic factors
 that explain why upscaled transport models fail to capture non-Fickian
 effects resulting from mean flow direction transience.
description: This research uses three models, detailed in the methods of the
 manuscript, and a brief description of the models and the data they rely
 on are provided below: hydraulic
 conductivity field: a T-PROGS (transition probability geostatistics)
 heterogeneous hydrofacies model of the Kings River Alluvial Fan. Model
 dimensions are 15 km 12.6 km x 100.5 m. The model was generated by a
 former study (Weissmann et al., 1999) and used data from well completion reports, borehole logs, and other geophysical logs. groundwater flow model: a MODFLOW-2000 groundwater flow model. a particle transport model: an RW3D model that solves the advection dispersion equation. The initial and boundary contditions of the models are specified in input files within the provided datasets, and detailed in the manuscript.
description: Detailed README.md files herein explain how to use the input
 files to re-produce the flow and transport models in this study.
DOI: 10.5061/dryad.2547d7wp4
title: Artificially selecting bacterial communities using propagule strategies

description: Artificial selection is a promising approach to manipulate microbial
 communities. Here, we report the outcome of two artificial selection
 experiments at the microbial community level. Both used “propagule”
 selection strategies, whereby the best-performing communities are used as
 the inocula to form a new generation of communities. Both experiments were
 contrasted to a random selection control. The first experiment used a
 defined set of strains as the starting inoculum, and the function under
 selection was the amylolytic activity of the consortia. The second
 experiment used multiple soil communities as the starting inocula, and the
 function under selection was the communities’ cross-feeding potential. In
 both experiments, the selected communities reached a higher mean function
 than the control. In the first experiment this was caused by a decline in
 function of the control, rather than an improvement of the selected line.
 In the second experiment, this response was fueled by the large initial
 variance in function across communities, and stopped when the
 top-performing community “fixed” in the metacommunity. Our results are in
 agreement with basic expectations from breeding theory, pointing to some
 of the limitations of community-level selection experiments which can
 inform the design of future studies.
DOI: 10.5061/dryad.3ffbg79gc
title: Data from: Macronutrient intake and simulated infection threat independently affect life history traits of male decorated crickets

description: Nutritional geometry has advanced our understanding of how macronutrients
 (e.g., proteins and carbohydrates) influence the expression of life
 history traits and their corresponding trade-offs. For example, recent
 work has revealed that reproduction and immune function in male decorated
 crickets are optimized at very different protein:carbohydrate (P:C)
 dietary ratios. However, it is unclear how an individual’s macronutrient
 intake interacts with its perceived infection status to determine
 investment in reproduction or other key life history traits. Here, we
 employed a fully factorial design in which calling effort and immune
 function were quantified for male crickets fed either diets previously
 demonstrated to maximize calling effort (P:C = 1:8) or immune function
 (P:C = 5:1), and then administered a treatment from a spectrum of
 increasing infection cue intensity using heat-killed bacteria. Both diet
 and a simulated infection threat independently influenced the survival,
 immunity, and reproductive effort of males. If they called, males
 increased calling effort at the low infection cue dose, consistent with
 the terminal investment hypothesis, but interpretation of responses at the
 higher threat levels was hampered by the differential mortality of males
 across infection cue and diet treatments. A high protein, low carbohydrate
 diet severely reduced the health, survival, and overall fitness of male
 crickets. There was, however, no evidence of an interaction between diet
 and infection cue dose on calling effort, suggesting that the threshold
 for terminal investment was not contingent on diet as investigated
 here.
DOI: 10.5061/dryad.0p2ngf1z6
title: Data from: Management actions shape dung beetle community structure and functional traits in restored tallgrass prairie

description: 1. Ecosystem restoration often focuses on reestablishing species richness
 and diversity of native organisms, especially plants. However, effective
 restoration requires re-establishment of ecosystem functions and processes
 by all trophic levels. Functional trait descriptions of communities,
 including decomposer communities, may provide more comprehensive
 evaluations of restoration activities and management than taxonomic
 community metrics alone. 2. We examined species and functional trait
 composition of dung beetle (Coleoptera: Scarabaeidae, Geotrupidae)
 communities across a  3-31 year chronosequence of restored
 prairies, in which sites varied in the presence of re-introduced bison and
 prescribed fire. We calculated functional diversity metrics and
 community-weighted mean trait values using behavioral and morphological
 measurements. We also performed a dung decomposition experiment to measure
 an ecosystem function driven by these insects. 3. Bison presence doubled
 beetle abundance and increased richness by 50%. Shannon diversity
 increased with restoration age, nearly doubling from the youngest to
 oldest restorations. Functional diversity was unchanged, except functional
 richness, which was reduced by bison and fire presence. Beetles were, on
 average, smaller in older restorations, although this pattern was weaker
 when bison were present. 4. Dung decomposition was unaffected by site
 characteristics but increased with community weighted mean beetle mass.
 Dung decomposition was better predicted by mean trait values, suggesting
 that supporting large-bodied species may be more important than species
 diversity in settings where maximizing decomposition function is a goal.
 5. Restoration managers should consider dung beetle communities and their
 functional characteristics when making management decisions, particularly
 where large grazers are a component of management strategies.
DOI: 10.5061/dryad.8931zcrnw
title: Brood parasitism, provisioning rates and breeding phenology of male and female magpie hosts

description: Parental care is a costly behaviour that raises the prospects of offspring
 survival. In species with biparental care these costs are shared by both
 parents, although there may be a conflict regarding the relative
 investment of each sex. Avian brood parasites leave all the costs of
 rearing offspring to their hosts. The magnitude of these costs and their
 consequences on the relative role of both sexes in parental care and
 future reproduction remain mostly unknown. Here, we investigate whether
 provisioning rate of nestlings by magpie hosts (Pica pica) differs between
 broods parasitized by the great spotted cuckoo (Clamator glandarius) and
 non-parasitized broods, and whether the relative contribution of each sex
 to provisioning is affected by parasitism. Furthermore, we explore the
 effect of parasitism on magpie’s future reproduction. We found that
 provisioning rate was similar in parasitized and non-parasitized broods,
 and that the relative contribution of males and females was also similar,
 irrespectively of the parasitism status. However, rearing parasitic
 offspring seems to have a negative long-term effect on magpie’s breeding
 phenology in the following breeding season. Our results suggest that,
 although brood parasitism by great spotted cuckoos does not seem to
 influence the relative contribution of both sexes to parental care, it may
 entail long-term extra costs in terms of breeding delay for magpies.