cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9cp1f
title: Data from: Dissecting the genetic architecture of F1 hybrid sterility in house mice

description: Hybrid sterility as a postzygotic reproductive isolation mechanism has
 been studied for over 80 years, yet the first identifications of hybrid
 sterility genes in Drosophila and mouse are quite recent. To study the
 genetic architecture of F_1 hybrid sterility between young subspecies of
 house mouse Mus m. domesticus and Mus m. musculus we conducted QTL
 analysis of a backcross between inbred strains representing these two
 subspecies and probed the role of individual chromosomes in hybrid
 sterility using the inter-subspecific chromosome substitution strains. We
 provide direct evidence that the asymmetry in male infertility between
 reciprocal crosses is conferred by the middle region of Mus m. musculus
 Chr X, thus excluding other potential candidates such as Y, imprinted
 genes, and mitochondrial DNA. QTL analysis identified strong hybrid
 sterility loci on Chr 17 and Chr X and predicted a set of interchangeable
 autosomal loci, a subset of which is sufficient to activate the
 Dobzhansky-Muller incompatibility of the strong loci. Overall, our results
 indicate the oligogenic nature of F_1 hybrid sterility, which should be
 amenable to reconstruction by proper combination of chromosome
 substitution strains. Such prefabricated model system should help to
 uncover the gene networks and molecular mechanisms underlying hybrid
 sterility.
description: Dissecting the genetic
 architecture of F1 hybrid sterility in PWD/Ph and C57BL/6J
 backcrossQTL mapping data in
 R/qtl format: BW = body weight [g], TW testes weight [mg], SC = sperm
 cells counted in Bürker chamber [millions]data.csvR scriptR script used for R/qtl mapping of "Dissecting the genetic architecture of F1 hybrid sterility in PWD/Ph and C57BL/6J backcross" datasetscript.R
DOI: 10.5061/dryad.212777q
title: Data from: Feedback between tissue packing and neurogenesis in the zebrafish neural tube

description: Balancing the rate of differentiation and proliferation in developing
 tissues is essential to produce organs of robust size and composition.
 Although many molecular regulators have been established, how these
 connect to physical and geometrical aspects of tissue architecture is
 poorly understood. Here, using high-resolution timelapse imaging, we find
 that changes to cell geometry associated with dense tissue packing play a
 significant role in regulating differentiation rate in the zebrafish
 neural tube. Specifically, progenitors that are displaced away from the
 apical surface due to crowding, tend to differentiate in a Notch-dependent
 manner. Using simulations we show that interplay between progenitor
 density, cell shape and changes in differentiation rate could naturally
 result in negative-feedback control on progenitor cell number. Given these
 results, we suggest a model whereby differentiation rate is regulated by
 density dependent effects on cell geometry to: (1) correct variability in
 cell number; and (2) balance the rates of proliferation and
 differentiation over development to ‘fill’ the available space.
description: Total.lsmThis is a xyzt confocal image set in the Zeiss lsm format. It is the raw data used in Figure 3C.
DOI: 10.5061/dryad.6nt37
title: Data from: Do flood pulses structure amphibian communities in floodplain environments?

description: Beta diversity can provide insights into the processes that regulate
 communities subjected to frequent disturbances, such as flood pulses,
 which control biodiversity in floodplains. However, little is known about
 which processes structure beta diversity of amphibians in floodplains.
 Here, we tested the influence of flood pulses on the richness,
 composition, and beta diversity of amphibians in Amazonian floodplain
 environments. We also evaluated indicator species for each environment. We
 established linear transects in three environments: low várzea, high
 várzea, and macrophyte rafts. Species richness decreased and beta
 diversity increased according to the susceptibility of habitats to flood
 pulses. Indicator species differed among environments according to forest
 succession promoted by the flood pulse. The decrease in species richness
 between high and low várzea is due to non-random extinctions. The higher
 rates of species turnover between várzeas and macrophyte rafts are driven
 by the colonization of species adapted to open areas. Our results
 highlight that the maintenance of complex environments is needed to
 protect biodiversity in floodplains.
description: MetadataData collected in floodplain environments of five oxbow lakes of a floodplain in the middle Purus river. We used this data to study the beta diversity and amphibian indicator species among environments of macrophyte rafts, high várza and low várzea. Legend for the lakes: BL, Bom Lugar; CA, Cametá; FO, Flor do Ouro; GU, Guama; SA, Santana.Metadados.xls
DOI: 10.5061/dryad.jh521
title: Data from: Evidence for repeated acquisition and loss of complex body form characters in an insular clade of Southeast Asian semi-fossorial skinks

description: Evolutionary simplification, or loss of complex characters, is a major
 theme in studies of body form evolution. The apparently infrequent
 evolutionary reacquisition of complex characters has led to the assertion
 (Dollo’s Law) that once lost, complex characters may be impossible to
 re-evolve, at least via the exact same evolutionary process. Here we
 provide one of the most comprehensive, fine-scale analyses of squamate
 body-form evolution to date, introducing a new model system of closely
 related, morphologically variable, lizards. Our phylogenetic results
 support independent instances of complete limb loss as well as multiple
 instances of digit and external ear opening loss and re-acquisition. Even
 more striking, we find strong statistical support for the re-acquisition
 of a pentadactyl body form from a digit-reduced ancestor. Our study
 reveals that species of the genus Brachymeles exemplify regions of
 morphospace (body plans) previously undocumented in squamates. Our
 findings have broad, general implications for body form evolution in
 burrowing vertebrates: whatever constraints have shaped trends in
 morphological evolution among other squamate groups (excluding Bipes) have
 been lost in this one exemplary clade. The results of our study join a
 nascent body of literature showing strong statistical support for complex
 character loss, followed by evolutionary re-acquisition of complex
 structures associated with a generalized pentadactyl body form.
description: Siler and Brown
 Morphometric DataThis is an excel file
 with morphological data used for this study. The file provides both the
 raw data as well as the natural log-transformed data. Log-transformed data
 columns are highlighted in blue. Each row corresponds to a species or
 lineage from the study. Column 1 provides the species/lineage name, with
 multiple lineages for a single species having locality
 identifiers.Siler_Brown_MorphometricData_Raw.xls
DOI: 10.5061/dryad.6h5b7
title: Data from: Habitat and social factors shape individual decisions and emergent group structure during baboon collective movement

description: For group-living animals traveling through heterogeneous landscapes,
 collective movement can be influenced by both habitat structure and social
 interactions. Yet research in collective behavior has largely neglected
 habitat influences on movement. Here we integrate simultaneous,
 high-resolution, tracking of wild baboons within a troop with a
 3-dimensional reconstruction of their habitat to identify key drivers of
 baboon movement. A previously unexplored social influence – baboons’
 preference for locations that other troop members have recently traversed
 – is the most important predictor of individual movement decisions.
 Habitat is shown to influence movement over multiple spatial scales, from
 long-range attraction and repulsion from the troop’s sleeping site, to
 relatively local influences including road-following and a short-range
 avoidance of dense vegetation. Scaling to the collective level reveals a
 clear association between habitat features and the emergent structure of
 the group, highlighting the importance of habitat heterogeneity in shaping
 group coordination.
description: data.zipCompressed file containing point cloud data and orthomosaic images of habitat used by baboons at Mpala Research Centre, Kenya. For associated baboon movement data, see: Crofoot MC, Kays RW, Wikelski M (2015) Data from: Shared decision-making drives collective movement in wild baboons. Movebank Data Repository. doi:10.5441/001/1.kn0816jn
DOI: 10.5061/dryad.fk0v0fq
title: Data from: Plant phenological asynchrony and community structure of gall-inducing insects associated with a tropical tree species

description: The dynamics of occurrence of target-organs in plant populations produces
 windows of opportunity that directly and indirectly affect the structure
 of herbivore communities. However, mechanisms that drive herbivore
 specialization between resource patches are still poorly known. In the
 present study, we tested three hypotheses related to variation in host
 plant phenology and community structure (i.e. composition, richness and
 abundance) of gall-forming species: (i) plants with early leaf-flushing in
 the season will have greater vegetative growth and high contents of
 secondary chemical compounds; (ii) gall-inducing insect community
 structure changes among temporary resource patches of the host and (iii)
 interspecific competition is a probable mechanism that drives
 gall-inducing insect community structure on Copaifera langsdorffii. We
 monitored daily a total of 102 individuals of the super-host C.
 langsdorffii from August 2012 to May 2013, to characterize the leaf
 flushing time of each host plant. The leaf flushing time had a positive
 relationship with the number of folioles per branch and a negative
 relationship with branch growth. We sampled a total of 4,906 galls
 belonging to 24 gall-inducing insect species from 102 individuals of C.
 langsdorffii. In spite of some gall-inducing species presented high
 abundance on early leaf-flushing plants, direct and indirect effects of
 plant phenology on galling insect abundance was species-dependent. At the
 community level, our study revealed that the quality and quantity of plant
 resources did not affect the richness and abundance of gall-inducing
 insects associated with C. langsdorffii. However, the richness and
 composition of gall-inducing species varied according to the variation in
 leaf flushing time of the host plant. The results of null model analysis
 showed that galls co-occurrence on C. langsdorffii trees differ more than
 expected by chance and that interspecific competition can be one potential
 mechanism structuring this gall-inducing insect community.
description: TableVariations in leaf
 flushing time, leaf phenol content, branch growth and abundance of 24
 species of gall-inducing insects associated with 102 Copaifera
 langsdorffii plants.tab.xls
DOI: 10.5061/dryad.g467j7g2
title: Data from: A framework for elucidating the temperature dependence of fitness

description: Climate warming is predicted to cause large-scale extinctions of
 ectothermic species. A striking difference between tropical and temperate
 ectotherms is that tropical species exhibit an upper temperature limit for
 survival (T_max) that is closer to the temperature at which fitness is
 maximized (T_opt). Thus, even a small increase in environmental
 temperature could put tropical ectotherms at high risk of extinction,
 whereas temperate ectotherms have a wider temperature cushion. Although
 this pattern is widely observed, the mechanisms that produce it are not
 well-understood. We develop a mathematical framework to partition the
 temperature response of fitness into its components (fecundity, mortality
 and development) and test model predictions with data for insects. We find
 that fitness declines at high temperatures because the temperature
 responses of fecundity and mortality act in opposite ways: fecundity
 decreases with temperature once temperatures exceed the optimal range,
 whereas mortality continues to increase. The proximity of T_opt to T_max
 depends on how the temperature response of development mediates the
 interaction between fecundity and mortality. When development is highly
 temperature-sensitive, mortality exceeds reproduction only after fecundity
 has started to decline with temperature, which causes fitness to decline
 rapidly to zero once temperatures exceed T_opt. The model correctly
 predicts empirically observed fitness-temperature relationships in insects
 from different latitudes. It potentially explains the widely-reported
 phenological shifts and latitudinal differences in fitness responses.
description: data_amarasekare&savage_2012Data on temperature responses of fecundity, mortality, development and intrinsic growth rate
DOI: 10.5061/dryad.7b2kg107
title: Data from: Interacting impacts of invasive plants and invasive toads on native lizards

description: The ecological impacts of an invasive species may be reduced by prior
 invasions if selective pressures imposed by earlier events preadapt the
 native biota to deal with the newer arrival. In northwestern Australia,
 invasion of the cane toad (Rhinella marina) kills many native predators if
 they ingest the highly toxic toads. Remarkably, the toads’ defensive
 toxins (bufadienolides) are chemically similar to those of another
 invasive species: an ornamental plant from Madagascar, Bryophyllum spp.
 (Crassulaceae, mother-of-millions). Omnivorous lizards (bluetongue skinks,
 Tiliqua scincoides) are imperiled by the invasion of toads in northwestern
 Australia, but conspecifics from other areas of the continent (those where
 exotic plants were introduced and including areas where toads have yet to
 invade) are less affected because they exhibit higher physiological
 tolerance of toad toxins (and also of plant toxins). The willingness of
 captive bluetongues to consume both toads and these plants and the high
 correlation in the lizards’ sensitivity to toad toxins versus plant toxins
 suggest that exotic plants may have imposed strong selection on the
 lizards’ physiological tolerance of bufadienolides. As a result,
 populations of lizards from areas previously exposed to these alien plants
 may be preadapted to deal with the toxins of the more recent anuran
 invader.
description: Sam's combined
 DATA, MOM onlyExcel file with
 reduction in lizard swimming speed following injection of synthetic
 bufalin. Columns show lizard IDs, collection localities, whether or not
 mother-of-millions (MOM) or cane toads occur in collection locality, and
 lizard mass and swim-speed (time) reduction.
DOI: 10.5061/dryad.q26g1
title: Data from: Opposite distortions in interval timing perception for visual and auditory stimuli with temporal modulations

description: When an object is presented visually and moves or flickers, the perception
 of its duration tends to be overestimated. Such an overestimation is
 called time dilation. Perceived time can also be distorted when a stimulus
 is presented aurally as an auditory flutter, but the mechanisms and their
 relationship to visual processing remains unclear. In the present study,
 we measured interval timing perception while modulating the temporal
 characteristics of visual and auditory stimuli, and investigated whether
 the interval times of visually and aurally presented objects shared a
 common mechanism. In these experiments, participants compared the
 durations of flickering or fluttering stimuli to standard stimuli, which
 were presented continuously. Perceived durations for auditory flutters
 were underestimated, while perceived durations of visual flickers were
 overestimated. When auditory flutters and visual flickers were presented
 simultaneously, these distortion effects were cancelled out. When auditory
 flutters were presented with a constantly presented visual stimulus, the
 interval timing perception of the visual stimulus was affected by the
 auditory flutters. These results indicate that interval timing perception
 is governed by independent mechanisms for visual and auditory processing,
 and that there are some interactions between the two processing systems.
description: Behavioral
 dataBehavioral data of each
 subjectrawdata.xls
DOI: 10.5061/dryad.nt65q
title: Data from: Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

description: Identifying phylogenetically distinct lineages and understanding the
 evolutionary processes by which they have arisen are important goals of
 phylogeography. This information can also help define conservation units
 in endangered species. Such analyses are being transformed by the
 availability of genomic-scale data sets and novel analytical approaches
 for statistically comparing different historical scenarios as causes of
 phylogeographic patterns. Here, we use genomic-scale
 restriction-site-associated DNA sequencing (RADseq) data to test for
 distinct lineages in the endangered Eastern Massasauga Rattlesnake
 (Sistrurus catenatus). We then use coalescent-based modeling techniques to
 identify the evolutionary mechanisms responsible for the origin of the
 lineages in this species. We find equivocal evidence for distinct
 phylogenetic lineages within S. catenatus east of the Mississippi River,
 but strong support for a previously unrecognized lineage on the western
 edge of the range of this snake, represented by populations from Iowa,
 USA. Snakes from these populations show patterns of genetic admixture with
 a nearby non-threatened sister species (Sistrurus tergeminus). Tests of
 historical demographic models support the hypothesis that the genetic
 distinctiveness of Iowa snakes is due to a combination of isolation and
 historical introgression between S. catenatus and S. tergeminus. Our work
 provides an example of how model-based analysis of genomic-scale data can
 help identify conservation units in rare species.
description: RAD3.txtFastq data fileRAD4.txtFastq data fileRAD5.txtFastq data fileRAD7.txtFastq data fileRAD9b.txtFastq data fileRAD14.txtFastq data fileRAD14.tar.gzRAD15.txtFastq data fileRAD16.txtFastq data fileRAD18.txtFastq data fileRAD19.txtFastq data fileRAD20.txtFastq data fileRAD21.txtFastq data fileRAD71.txtFastq data fileClustering_SNAPP_BarcodeFiles.tarBarcode files (Individual sample names and associated barcode/molecular identifier) associated with clustering and SNAPP runs. Formatted for analysis with AftrRAD.fsc_BarcodeFiles.tarBarcode files (Individual sample names and associated barcode/molecular identifier) associated with fastsimcoal runs. Formatted for analysis with AftrRAD.
DOI: 10.5061/dryad.2d95h
title: Data from: An ecological approach to measuring the evolutionary consequences of gene flow from crops to wild or weedy relatives

description: Premise of the study: Agricultural practices routinely create
 opportunities for crops to hybridize with wild relatives, leading to crop
 gene introgression into wild genomes. Conservationists typically worry
 this introgression could lead to genetic homogenization of wild
 populations, over and above the central concern of transgene escape.
 Alternatively, viewing introgression as analogous to species invasion, we
 suggest that increased genetic diversity may likewise be an undesirable
 outcome. Methods: Here, we compare the sensitivity of conventional
 population genetic metrics with species diversity indices as indicators of
 the impact of gene flow on genetic diversity. We illustrate this novel
 approach using multilocus genotype data (12 allozyme loci) from 10 wild
 (Beta vulgaris subsp. maritima) and eight putative crop–wild hybrid beet
 populations (B. vulgaris subsp. vulgaris × B. vulgaris subsp. maritima)
 scattered throughout Europe. Results: Conventional population genetic
 metrics mostly failed to detect shifts in genetic composition of putative
 hybrid populations. By contrast, species diversity indices unambiguously
 revealed increased genetic diversity in putative hybrid populations.
 Discussion: We encourage other workers to explore the utility of our more
 sensitive approach for risk assessment prior to the release of transgenic
 crops, with a view toward widespread adoption of our method in studies
 aimed at detecting allelic invasion.
description: Genotyped Beta vulgaris
 after Structure ClusteringThis file contains
 allozyme genotypes of Beta vulgaris individuals collected from cultivated
 (ssp. vulgaris), wild (ssp. maritima), and putative crop-wild hybrid
 populations in Europe.
DOI: 10.5061/dryad.br52k
title: Data from: Hepcidin-25 in diabetic chronic kidney disease is predictive for mortality and progression to end stage renal disease

description: Background: Anemia is common and is associated with impaired clinical
 outcomes in diabetic chronic kidney disease (CKD). It may be explained by
 reduced erythropoietin (EPO) synthesis, but recent data suggest that
 EPO-resistance and diminished iron availability due to inflammation
 contribute significantly. In this cohort study, we evaluated the impact of
 hepcidin-25—the key hormone of iron-metabolism—on clinical outcomes in
 diabetic patients with CKD along with endogenous EPO levels. Methods: 249
 diabetic patients with CKD of any stage, excluding end-stage renal disease
 (ESRD), were enrolled (2003–2005), if they were not on EPO-stimulating
 agent and iron therapy. Hepcidin-25 levels were measured by
 radioimmunoassay. The association of hepcidin-25 at baseline with clinical
 variables was investigated using linear regression models. All-cause
 mortality and a composite endpoint of CKD progression (ESRD or doubling of
 serum creatinine) were analyzed by Cox proportional hazards models.
 Results: Patients (age 67 yrs, 53% male, GFR 51 ml/min, hemoglobin 131
 g/L, EPO 13.5 U/L, hepcidin-25 62.0 ng/ml) were followed for a median time
 of 4.2 yrs. Forty-nine patients died (19.7%) and forty (16.1%) patients
 reached the composite endpoint. Elevated hepcidin levels were
 independently associated with higher ferritin-levels, lower EPO-levels and
 impaired kidney function (all p&lt;0.05). Hepcidin was related to
 mortality, along with its interaction with EPO, older age, greater
 proteinuria and elevated CRP (all p&lt;0.05). Hepcidin was also
 predictive for progression of CKD, aside from baseline GFR, proteinuria,
 low albumin- and hemoglobin-levels and a history of CVD (all
 p&lt;0.05). Conclusions: We found hepcidin-25 to be associated with
 EPO and impaired kidney function in diabetic CKD. Elevated hepcidin-25 and
 EPO-levels were independent predictors of mortality, while hepcidin-25 was
 also predictive for progression of CKD. Both hepcidin-25 and EPO may
 represent important prognostic factors of clinical outcome and have the
 potential to further define “high risk” populations in CKD.
description: dataset_Wagner_Hepcidin-25_in_diabetic_CKDdataset.zip
DOI: 10.5281/zenodo.18385262
title: Unexpected Biomagnification of Neonicotinoids in Antarctic Food Webs Driven by Latitude
DOI: 10.5281/zenodo.18385263
title: Unexpected Biomagnification of Neonicotinoids in Antarctic Food Webs Driven by Latitude