cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sf7m0cjm
title: Vegetation growth and landscape genetics of Tillandsia lomas at its dry limits in the Atacama Desert shows fine-scale response to environmental parameters

description: 1. Ecosystems at its dry limits have been studied while focusing on
 species biology, fitness and interactions of biotic and abiotic
 parameters; however, the interactive effects of these parameters remain
 under-explored and, therefore, information is often lacking about the
 putative effect of global climate change on these ecosystems. 2. Here, we
 conducted an analysis of the interplay of fine-scale landscape genetics
 and biotic and abiotic factors of terrestrial Tillandsia lomas in the
 hyperarid Atacama Desert, characterized by a fog-dependent vegetation type
 consisting of almost one single vascular plant species only. 3. We showed
 that metapopulations of Tillandsia landbeckii are genetically connected
 over many hundreds of squarekilometres, and despite a large potential to
 propagate clonally genetic diversity is structured, regionally and
 locally. On landscape-level genetic diversity correlates well with fitness
 parameters such as growth, flowering and vegetation density, and we
 observed also fine-scaled correlation with a 3-D landscape model
 indicating a positive feedback with saisonal fog occurrence and
 availability. The various interdependies of biotic and abiotic factors
 also result in regular linear banding patterns of vegetation arranged
 orthogonally towards landscape slope. Ex-situ growth experiments indicate
 that T. landbeckii growths at optimal rates within this extreme, hyperarid
 environment, and we can extrapolate mean biomass production for this
 particular ecosystem. 4. Synthesis. Our results suggest that the unique
 ecosystem of terrestrial Tillandsia lomas in the hyperarid Atacama Desert
 is an evolutionary balanced and fine-scaled system. Vegetation itself is
 built up by long-lived and persistent modules. We developed a descriptive
 model of the various interacting factors, thereby highlighting also a
 severe threat caused by global climate change.
description: <b>The data
 supplements contain
 (</b>Tillandsia_Supplement_Data_Dryad.docx)   <b>a) AFLP data set
 1</b> AFLPs_Data_set_1_metapopulation.nex <b>This is a nexus file of 0/1 matrix from AFLP analysis comprising a set of individuals from the metapolulation around Iquique (Chile) plus Peruvian outgroup material.</b>   <b>b) AFLP data set 2</b> AFLPs_Data_set_2.xlsx <b>This excel-file shows the AFLP scoring results from Oyarbide study field comprising Tillandsia landbeckii only.</b>   <b>c) Seasonal growth data at Oyarbide</b> Growth_screening_Oyarbide.xlsx <b>The file contains saisonal growth data from the 9 permanent study plots. Red indicates total failure (individual label destroyed by wind and/or sand). Orange indicate loss of data fragments, but measurements were able because of new calibration. </b> <b>Translation key provided in Growth_screening_Oyarbide_translation_key.rtf</b>
DOI: 10.5061/dryad.bnzs7h47h
title: Data from: Avian developmental rates are constrained by latitude and migratoriness – a global analysis

description: Aim: It has long been recognized that tropical bird species demonstrate a
 wide range of traits characteristic for slow life histories, as indicated
 by lower investment in reproduction, slower senescence or slower
 physiological pace of life. Nevertheless, evidence for latitudinal
 variation in avian developmental rates has, so far, been inconclusive and
 based on limited geographic or phylogenetic sampling. The aim of this
 study was to test for global associations of avian developmental rates
 with latitude and migratoriness. Location: Global. Taxon: Birds. Methods:
 We compiled data on developmental (incubation and fledging) periods of
 3500 passerine and non-passerine bird species distributed worldwide, which
 represented nearly all extant avian orders and families. Associations of
 developmental periods with latitude and migratoriness were analysed with
 phylogenetically-informed comparative models that controlled for major
 sources of variation in developmental rates (body mass, clutch size, and
 developmental mode across altricial-precocial spectrum). Results: Our
 analyses provided support for a negative latitudinal gradient in the
 duration of fledging, but not incubation period. After controlling for
 latitude, we also found that migratory birds showed faster developmental
 rates than resident species. Finally, we found that developmental rates
 were non-linearly associated with clutch size (fastest developmental rates
 at intermediate clutch size) and that duration of fledging period had
 higher evolutionary lability than incubation period. Main conclusions: Our
 global comparative analysis provided convincing and
 phylogenetically-robust evidence for a long-held hypothesis on latitudinal
 variation in avian developmental rates, although the pattern was apparent
 only at the post-embryonic stage of development (fledging period). This
 challenges a common belief on longer incubation periods in tropics and
 indicates that incubation and fledging periods may differently respond to
 external environmental factors, which can possibly be driven by their
 different evolutionary lability. The results may contribute to our
 understanding of biogeographic variation in species diversity.
DOI: 10.15151/esrf-es-2296888318
title: Coherent Diffraction Imaging of Three-dimensional strain fields in qubit devices

description: Electron spin qubits in (Si,Ge)/Si/(Si,Ge) heterostructures are based on quantum dots (QDs) defined by the strain of the Si quantum well (QW) plus electrostatic gates. Spin coherent shuttling over several microns is possible by applying time-dependent waveforms to an additional series of connecting clavier gates [1]. Strain fluctuations on the 100 nm level deteriorate the uniformity of electron potential and may lead to decoherence. On the other hand, engineering certain components of the strain tensor may be used to increase the valley splitting – the critical parameter defining the qubit operation temperature [2]. As we showed by Scanning X-ray Diffraction Microscopy (SXDM), a significant source of strain is the stress exerted by the gate electrodes themselves. Here, we propose to use coherent Bragg diffraction to investigate finely resolved 3D strain fields in shuttling devices (“QuBus”) with structure sizes smaller than the beam.
DOI: 10.5061/dryad.s4mw6m94f
title: Data from: De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in Amanita

description: By introducing novel capacities and functions, new genes and gene families
 may play a crucial role in ecological transitions. Mechanisms generating
 new gene families include de novo gene birth, horizontal gene transfer and
 neofunctionalization following a duplication event. The ectomycorrhizal
 (ECM) symbiosis is a ubiquitous mutualism and the association has evolved
 repeatedly and independently many times among the fungi, but the molecular
 dynamics enabling its emergence remain elusive. We developed a
 phylogenetic workflow to first understand if gene families unique to ECM
 Amanita fungi and absent from closely related asymbiotic species are
 functionally relevant to the symbiosis, and then to systematically infer
 their origins. We identified 109 gene families unique to ECM Amanita
 species. Genes belonging to unique gene families are under strong
 purifying selection and are upregulated during symbiosis, compared to
 genes of conserved or orphan gene families. The origins of seven of the
 unique gene families are strongly supported as either de novo gene birth
 (two gene families), horizontal gene transfer (four), and gene duplication
 (one). An additional 34 families appear new because of their selective
 retention within symbiotic species. Among the 109 unique gene families,
 the most upregulated gene in symbiotic cultures encodes an ACC deaminase,
 an enzyme capable of downregulating the synthesis of the plant hormone
 ethylene. Ethylene is a common negative regulator of plant-microbial
 mutualisms.
description: analytical results scripts
 README
DOI: 10.5061/dryad.0p2ngf1xc
title: Data from: A comparative test for divergent adaptation: inferring speciation drivers from functional trait divergence

description: Ecological differentiation between lineages is widely considered to be an
 important driver of speciation. However, support for this hypothesis is
 largely derived from the detailed study of a select set of model species
 pairs. Mounting evidence from non-model taxa, meanwhile, suggests that
 speciation often occurs with minimal differentiation in ecomorphology,
 calling into question the true contribution of divergent selection to
 species richness in nature. To better understand divergent adaptation and
 its role in speciation generally, researchers require a comparative
 approach that can distinguish its signature from alternative processes
 such as drift and parallel selection in datasets containing many species
 pairs. Here we introduce the first statistical models of divergent
 adaptation in the continuous traits of paired lineages. In these models,
 ecomorphological characters diverge as two lineages adapt toward
 alternative phenotypic optima following their departure from a common
 ancestor. The absolute distance between optima measures the extent of
 divergent selection and provides a basis for interpretation. We encode the
 models in the new R-package diverge and extend them to allow the distance
 between optima to vary across continuous and categorical variables. We
 test model performance using simulation and demonstrate model application
 using published datasets of trait divergence in birds and mammals. Our
 framework provides the first explicit test for the signature of divergent
 selection in trait divergence datasets, and it will enable empiricists
 from a wide range of fields to more fully investigate the dynamics of
 divergent adaptation as well as its prevalence in nature beyond just our
 best-studied model systems.
description: These are previously published data used in the example analyses
 of the present paper, which is a model description. They are brought
 together here for the convenience of readers wishing to repeat these
 analyses.
DOI: 10.5061/dryad.msbcc2fvq
title: Data from: Recovery of a boreal ground-beetle (Coleoptera: Carabidae) fauna 15 years after variable retention harvest

description: 1. Retention harvests are preferred over traditional clear-cuts for
 sustainable forest management because maintenance and re-establishment of
 native forest biodiversity is a priority. However, few studies have
 examined long-term responses of biotic assemblages to retention harvest at
 particular sites. 2. We studied the effects of decreasing initial harvest
 intensities (clear-cut, 10, 20, 50, and 75% dispersed green tree
 retention) on carabid beetle assemblages relative to assemblage changes in
 un-harvested control stands in four successionally ordered cover-types of
 boreal mixedwood forest. We also studied temporal effects by comparing
 assemblages over a 16-year pre- and post-harvest period, using data
 collected through monitoring of the EMEND (Ecosystem Management Emulating
 Natural Disturbance) experiment in NW Alberta, Canada. 3. Retention
 harvests affected assemblages differently across cover-types. Assemblages
 in compartments harvested in the earlier forest successional stages of
 ‘deciduous’ or ‘deciduous with spruce understory’ converged toward the
 pre-harvest structure of corresponding controls over time. In contrast,
 beetle assemblages in ‘mixed’ or ‘conifer’ compartments, that represent
 later successional forest, moved steadily away from their pre-harvest
 structures during the first post-harvest decade. These latter assemblages
 became strikingly more similar to those under deciduous canopies by 15
 years post-harvest. Synthesis and applications. Variable retention
 harvests will promote and maintain biodiversity better than clear-cutting.
 Higher retention levels promote faster recovery, but toward fauna typical
 of early successional forest in all cover-types. Carabids associated with
 conifer habitats are less resistant to impact from harvesting than are
 those from broadleaf deciduous forest. Therefore, conifer dominated stands
 present the most significant management challenge and higher retention
 levels are required to promote rapid and effective faunal recovery in such
 late successional stands.
description: Ground-beetles were collected at the same sites in all EMEND
 compartments using pitfall traps in 1999, 2000, 2004, 2009 and 2014, with
 these years corresponding to 1, 2, 5, 10 and 15 years post-harvest,
 respectively. Pre-harvest sampling (1998) was more limited, but
 ground-beetles were also sampled more widely across the stands originally
 designated as replicate blocks for each cover-type.
 Ground-beetles were pooled by compartment across each year's
 collection. Catches were standardized to number of individuals per 100
 trap-days to minimize effects of occasional trap disturbance on the
 data. Canonical Redundancy Analysis (RDA; Legendre and
 Legendre 2012) was used to assess the response of ground-beetle assemblage
 composition to three factors (time, cover-type, harvest treatment and
 their interactions).
description: EMEND Carabids abundance data (1998-2014)
DOI: 10.5061/dryad.cnp5hqc2k
title: Data from: Different genetic basis for ADH activity and plasticity in a novel alcohol environment for Drosophila melanogaster

description: Phenotypic plasticity is known to enhance population persistence (Wang and
 Althoff, 2019), facilitate adaptive evolution (Levis et al., 2018), and
 initiate novel phenotypes in novel environments (Levis and Pfennig, 2016).
 How plasticity can contribute or hinder adaptation to different
 environments hinges on its genetic architecture. Even though plasticity in
 many traits is genetically controlled, whether and how plasticity’s
 genetic architecture might change in novel environments is still unclear.
 Because much of gene expression can be environmentally influenced, each
 environment may trigger different sets of genes that influence a trait.
 Using a quantitative trait loci (QTL) approach, we investigated the
 genetic basis of plasticity in a classic functional trait, alcohol
 dehydrogenase (ADH) activity in D. melanogaster, across both historical
 and novel alcohol environments. Previous research in D. melanogaster has
 also demonstrated that ADH activity is plastic in response to alcohol
 concentration in substrates used by both adult flies and larvae. We found
 that across all environments tested, ADH activity was largely influenced
 by a single QTL encompassing the Adh coding gene and its known regulatory
 locus, delta-1. After controlling for the allelic variation of the Adh and
 delta-1 loci, we found additional but different minor QTLs in the 0% and
 14% alcohol environments. In contrast, we discovered no major QTL for
 plasticity itself, including the Adh locus, regardless of the
 environmental gradients. This suggests that plasticity in ADH activity is
 likely influenced by many loci with small effects and that the Adh locus
 is not environmentally sensitive to dietary alcohol.
description: We measured larval alochol dehydrogenase activity in 0%, 7%, and
 14% alcohol environments.
description: All analysis were done in the R (3.6.1) environment. The file
 "Analysis.R" contains code used to clean, process, and analyzed
 the data, and the file "Figures.R" contains code used to
 generate the figures for the related manuscript. Please see the related
 manuscript for more details.
DOI: 10.5061/dryad.41ns1rnbb
title: Data from: Developing a Stopover-CORT hypothesis: corticosterone predicts body composition and refueling rate in Gray Catbirds during migratory stopover

description: Migratory flight is energetically challenging, requiring alternating
 phases of fuel catabolism and fuel accumulation, accompanied by dramatic
 changes in body composition and behavior. Baseline corticosterone (CORT;
 the primary glucocorticoid in birds) is thought to underlie transitions
 between fuel catabolism during flight, fuel deposition during stopover,
 and the initiation of migratory flight. However, studies of CORT on
 stopover physiology and behavior remain disparate efforts, lacking the
 cohesion of a general hypothesis. Here we develop a Stopover-CORT
 hypothesis formalizing the relationships among CORT, body condition, and
 refueling rate in migratory birds. First we expect body mass to increase
 with triglycerides (TRIG) as birds refuel. Second, based on a synthesis of
 previous literature, we predict a U-shaped CORT curve over the course of
 stopover, postulating that elevated CORT at arrival is reactive,
 responding to poor body condition, while CORT elevation before departure
 is preparative, driving changes in behavior and body condition. We tested
 these predictions in Gray Catbirds (Dumetella carolinensis) following a
 trans-Gulf flight during spring migration. We found baseline CORT was
 negatively correlated with body condition and TRIG, corresponding with our
 predictions for arriving and refueling—but not departing—birds. It is
 possible catbirds undergo regional habitat translocations rather than
 complete the entire stopover phase at our study site. We propose the
 Stopover-CORT hypothesis as a useful predictive framework for future
 studies of the mechanistic basis of stopover physiology. By studying the
 regulation of stopover refueling and departure, we may better understand
 physiological limitations to overall migration rate and improve
 assessments of habitat quality for refueling birds.
description: min_day_of_stopover: The minimum possible day of stopover, based on recapture data (=days since initial capture) CORT_adj: the value used in analyses--raw CORT data from the assay, adjusted for recoveries QMR_Mean_Lean and QMR_Mean_Fat: the average lean mass and fat mass values from repeated (2-3) QMR scans for each individual Min_to_bleed: the blood sample was collected this many minutes after the bird's capture was observed Bleed_Time_min: the time of day (in minutes) when the blood sample was collected atypical: whether or not the individual was considered to have body composition not typical of a trans-Gulf migrant, based on lean mass residuals and fat mass (see Methods)
DOI: 10.5061/dryad.7m0cfxpr5
title: Data from: Species-area relationships in the Andaman and Nicobar islands emerge because rarer species are disproportionately favored on larger islands

description: The Island Species-Area relationship (ISAR) describes how the number of
 species increases with increasing size of an island (or island-like
 habitat), and is of fundamental importance in island biogeography and
 conservation. Here, we use a framework based on individual-based
 rarefaction to infer whether ISARs result from passive sampling, or
 whether some processes are acting beyond sampling (e.g., disproportionate
 effects and/or habitat heterogeneity). Using data on total and relative
 abundances of four taxa (birds, butterflies, amphibians and reptiles) from
 multiple islands in the Andaman and Nicobar archipelago, we examine how
 different metrics of biodiversity (total species richness, rarefied
 species richness, and abundance-weighted effective numbers of species
 emphasizing common species) vary with island area. Total species richness
 increased for all taxa, as did rarefied species richness controlling for a
 given sampling effort. This indicates that the ISAR did not result because
 of passive sampling, but that instead, some species were
 disproportionately favored on larger islands. For birds, frogs and
 lizards, this disproportionate effect was only associated with species
 that were rarer in the samples, but for butterflies, both more common and
 rarer species were affected. Furthermore, for the two taxa for which we
 had plot-level data (reptiles and amphibians), within-island β-diversity
 did not increase with island size, suggesting that within island
 compositional effects were unlikely to be driving these ISARs. Overall,
 our results indicate that the ISARs of these taxa are most likely driven
 by disproportionate effects, that is, where larger islands are important
 sources of biodiversity beyond a simple sampling expectation, especially
 through their influence on rarer species, thus emphasizing their role in
 the preservation and conservation of species.
description: For more details on the methods for data collection, see Davidar
 et al. (1996) and Devy et al. (1998) for birds and butterflies, and
 Surendran and Vasudevan (2015) for data collection of the frogs and
 lizards. References: 
 Davidar, P., Y. K, G. Tg, and N. Joshi. 1996. An assessment of
 common and rare forest bird species of the Andaman Islands. Forktail
 12:99–105. Devy, M. S., T. Ganesh, and P. Davidar.
 1998. Patterns of butterfly distribution in the Andaman islands:
 implications for conservation. Acta Oecologica 19:527–534.
 Surendran, H., and K. Vasudevan. 2015. The devil is in the
 detail: estimating species richness, density, and relative abundance of
 tropical island herpetofauna. BMC Ecology 15.
description: Data files for birds and butterflies are pooled abundances (i.e.,
 total abundances of species per island). Data files for lizards and frogs
 are plot-level abundance data (i.e., abundance of species per plot per
 island).
DOI: 10.25338/b8162m
title: Data from: Feeding and damage-induced volatile cues make beetles disperse and produce a more even distribution of damage for sagebrush

description: 1. Induced plant responses to herbivory are common and we have learned a
 lot about the mechanisms of induced resistance and their effects on
 herbivore performance.  We know less about their effects on
 herbivore behavior and especially on spatial patterns of damage. 2.
 Theoretical models predict that induced responses can cause patterns of
 damage to become aggregated, random, or even.  A recent model
 predicted that informed herbivore movement coupled with communication
 between plants would make damage more even within individual
 plants.  We tested these predictions in the field using a
 specialist beetle (Trirhabda pilosa) that feeds on sagebrush (Artemisia
 tridentata). Both the beetle and the plant are well-documented to respond
 to damage-induced volatile cues. 3. Beetle larvae were more likely to move
 from damaged leaves and leaves that had been exposed to volatiles from
 nearby damaged leaves compared to undamaged control leaves. 
 Previous lab results indicated that beetles were more likely to choose
 undamaged leaves compared to damaged leaves or those exposed to volatile
 cues of damage. 4. A comparison of damage patterns early in the season and
 after completion of beetle feeding revealed that variance in damage among
 branches decreased as the season progressed; i.e., damage became more
 evenly distributed among the branches within a plant.  Larvae
 damaged many leaves on a plant but removed relatively little tissue from
 each leaf. 5. Herbivore movement and the spatial patterns of damage that
 it creates can be important in determining effects on plant fitness and
 other population processes.  Dispersion of damage deserves more
 consideration in plant-herbivore studies.
description: Data for figure 1 are in the file sagebeetledam.xlsx
 Data for figure 5 are in the file Distribution_of
 _damage_10_bushes.xlsx, sheet 2. Jdam in column C is the number of leaves
 that had damage during the July survey. Jtot in column D is the total
 number of leaves on each branch during the July survey. Adam in column E
 is the number of leaves that had damage during the August survey. Atot in
 column G is the total number of leaves on each branch during the August
 survey. Prodam in columns G, H is the proportion of leaves with damage
 during July and August respectively.