cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bv13
title: Data from: Requirements and limits of anatomy-based predictions of locomotion in terrestrial arthropods with emphasis on arachnids

description: Modern computer-aided techniques foster the availability and quality of 3D
 visualization and reconstruction of extinct and extant species. Moreover,
 animated sequences of locomotion and other movements find their way into
 motion pictures and documentary films, but also gain attraction in
 science. While movement analysis is well advanced in vertebrates,
 particularly in mammals and birds, analyses in arthropods, with their much
 higher variability regarding general anatomy and size, are still in their
 infancies and restricted to a few laboratory species. These restrictions
 and deficient understanding of terrestrial arthropod locomotion in general
 impedes sensible reconstruction of movements in those species that are not
 directly observable (e.g., extinct and cryptic species). Since
 shortcomings like over-simplified approaches to simulate arthropod
 locomotion became obvious recently, in this review we provide insight into
 physical, morphological, physiological, behavioral, and ecological
 constraints, which are essential for sensible reconstructions of
 terrestrial arthropod locomotion. Such concerted consideration along with
 sensible evaluations of stability and efficiency requirements can pave the
 way to realistic assessment of leg coordination and body dynamics.
description: gamasid_slowed
 down_50timesThe video shows a
 gamasid mite running at 8.1 mm/s with duty factors of about 0.72 and
 ipsilateral phase shifts between adjacent legs of about 0.49. The body
 length of the specimen was about 1.3 mm. The sequence is slowed down to
 1/50 of the recording speed.trombidid_slow_slowed
 down_50timesA trombidid mite (body
 length: about 0.8 mm) running at about 34 mm/s with duty factors of about
 0.57 and ipsilateral phase shifts of about 0.53. The sequence is slowed
 down to 1/50 of the recording speed.trombidid_quick_slowed
 down_50timesA trombidid mite (body
 length about 0.8 mm) running at about 42 mm/s with duty factors of about
 0.54 and ipsilateral phase shifts of about 0.59. The sequence is slowed
 down to 1/50 of the recording speed.
DOI: 10.5281/zenodo.18147120
title: A Generic Residue-Numbering system for Microbial Rhodopsins
DOI: 10.5281/zenodo.18147121
title: A Generic Residue-Numbering system for Microbial Rhodopsins
DOI: 10.5061/dryad.r3s14
title: Data from: Shaped by the past, acting in the present: transgenerational plasticity of anti-predatory traits

description: Phenotypic expression can be altered by direct perception of environmental
 cues (within-generation phenotypic plasticity) and by the environmental
 cues experienced by previous generations (transgenerational plasticity).
 Few studies, however, have investigated how the characteristics of
 phenotypic traits affect their propensity to exhibit plasticity within and
 across generations. We tested whether plasticity differed within and
 across generations between morphological and behavioral anti-predator
 traits of Physa acuta, a freshwater snail. We reared 18 maternal lineages
 of P. acuta snails over two generations using a full factorial design of
 exposure to predator or control cues and quantified adult F2 shell size,
 shape, crush resistance, and anti-predator behavior - all traits which
 potentially affect their ability to avoid or survive predation attempts.
 We found that most morphological traits exhibited transgenerational
 plasticity, with parental exposure to predator cues resulting in larger
 and more crush-resistant offspring, but shell shape demonstrated
 within-generation plasticity. In contrast, we found that anti-predator
 behavior expressed only within-generation plasticity such that offspring
 reared in predator cues responded less to the threat of predation than
 control offspring. We discuss the consequences of this variation in
 plasticity for trait evolution and ecological dynamics. Overall, our study
 suggests that further empirical and theoretical investigation is needed in
 what types of traits are more likely to be affected by within-generational
 and transgenerational plasticity.
description: CrushSnailSheetThis was the data sheet used to examine the explanatory variables influencing crush resistance. Columns included are: "Snail.ID.no" = snail ID number, "Newton" = force required to break shell, "line" = maternal snail line, "numberincup" = snail density in each housing arena, "Dvpop" = divergence vector, "centroid" = sizeF2_Behavior_WMorphologyThis file contains the results of anti-predator behavioral trials and morphological measures for those individuals. "snail.ID" = individual snail ID, "Condition" = pre- or post-cue addition, "check.number" = observation number before or after the addition of cue, "centroid" = size, "Dvpop" = divergence vector, "numberincup" = snail density in home arena, "line" = maternal line, "Treatment" = F2 treatment (C = control, P = predator), "Treatment.parent" = F1 treatment (C = control, P = predator)morphoanalysisF2DVsThis file was used to look for a treatment (F1 and F2) on morphology (shape and size). Columns included are: "centroid" = size, "Dvpop" = divergence vector, "line" = maternal line, "treatment" = F2 treatment (C = control, P = predator), "ptreatment" = F1 treatment (C = control, P = predator), "numberincup" = snail density in home arenas
DOI: 10.15468/dl.kd7ddw
title: Occurrence Download

description: A dataset listing the 27329 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.11481 42.44298,3.12553 42.36672,3.23451 42.28316,3.12118 42.28288,3.05566 42.1582,3.14987 42.09981,3.16687 41.90474,3.04609 41.83882,2.91592 41.74382,2.71966 41.65841,2.51209 41.60017,2.23976 41.46312,2.10505 41.33339,1.91366 41.29376,1.31765 41.16957,0.98077 41.07968,0.6358 40.77902,0.79567 40.69512,0.59306 40.65417,0.48175 40.53177,1.33696 40.44892,2.41018 40.81442,3.53639 41.48042,3.93302 41.93621,3.60343 42.44902,3.33303 42.43351,3.11481 42.44298))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 27329 records were derived from 620 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001426-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j4r56
title: Data from: Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards

description: Recent radiations are important to evolutionary biologists, because they
 provide an opportunity to study the mechanisms that link micro- and
 macroevolution. The role of ecological speciation during adaptive
 radiation has been intensively studied, but radiations can arise from a
 diversity of evolutionary processes; in particular, on large continental
 landmasses where allopatric speciation might frequently precede ecological
 differentiation. It is therefore important to establish a phylogenetic and
 ecological framework for recent continental-scale radiations that are
 species-rich and ecologically diverse. Here, we use a genomic (approx. 1
 200 loci, exon capture) approach to fit branch lengths on a
 summary-coalescent species tree and generate a time-calibrated phylogeny
 for a recent and ecologically diverse radiation of Australian scincid
 lizards; the genus Cryptoblepharus. We then combine the phylogeny with a
 comprehensive phenotypic dataset for over 800 individuals across the 26
 species, and use comparative methods to test whether habitat
 specialization can explain current patterns of phenotypic variation in
 ecologically relevant traits. We find significant differences in
 morphology between species that occur in distinct environments and
 convergence in ecomorphology with repeated habitat shifts across the
 continent. These results suggest that isolated analogous habitats have
 provided parallel ecological opportunity and have repeatedly promoted
 adaptive diversification. By contrast, speciation processes within the
 same habitat have resulted in distinct lineages with relatively limited
 morphological variation. Overall, our study illustrates how alternative
 diversification processes might have jointly stimulated species
 proliferation across the continent and generated a remarkably diverse
 group of Australian lizards.
description: Concatenated alignment
 of exonic sequence dataConcatenated alignment
 (1195 loci) of exonic sequence data used to fit branch length on
 summary-coalescent species tree20150910_alignment.phyMorphological datasetPhenotypic measurements used to infer morphological evolutionmorph_data.csv
DOI: 10.5061/dryad.gs8r2
title: Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi

description: Wolbachia is a maternally inherited and ubiquitous endosymbiont of
 insects. It can hijack host reproduction by manipulations such as
 cytoplasmic incompatibility (CI) to enhance vertical transmission.
 Horizontal transmission of Wolbachia can also result in the colonization
 of new mitochondrial lineages. In this study, we present a 15-year-long
 survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across
 Europe and the spatiotemporal distribution of two prevalent strains, wCer1
 and wCer2, and associated mitochondrial haplotypes in Germany. Across most
 of Europe, populations consisted of either 100% singly (wCer1) infected
 individuals with haplotype HT1, or 100% doubly (wCer1&2) infected
 individuals with haplotype HT2, differentiated only by a single nucleotide
 polymorphism. In central Germany, singly infected populations were
 surrounded by transitional populations, consisting of both singly and
 doubly infected individuals, sandwiched between populations fixed for
 wCer1&2. Populations with fixed infection status showed perfect
 association of infection and mitochondria, suggesting a recent CI-driven
 selective sweep of wCer2 linked with HT2. Spatial analysis revealed a
 range expansion for wCer2 and a large transition zone in which wCer2
 splashes appeared to coalesce into doubly infected populations.
 Unexpectedly, the transition zone contained a large proportion (22%) of
 wCer1&2 individuals with HT1, suggesting frequent intraspecific
 horizontal transmission. However, this horizontal transmission did not
 break the strict association between infection types and haplotypes in
 populations outside the transition zone, suggesting that this horizontally
 acquired Wolbachia infection may be transient. Our study provides new
 insights into the rarely studied Wolbachia invasion dynamics in field
 populations.
description: Microsatellite raw
 dataMicrosat_FragAnalysis_rawdata.zipFstat dataFstat.zipStructure dataStructure.zipGenAlExRc Micros D GenAlEx.xlsmtDNA sequencesSequences.zip
DOI: 10.5061/dryad.sh2mb
title: Data from: Genome-wide association study in Arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants

description: Seed oil melting point is an adaptive, quantitative trait determined by
 the relative proportions of the fatty acids that compose the oil. Micro-
 and macro-evolutionary evidence suggests selection has changed the melting
 point of seed oils to covary with germination temperatures because of a
 trade-off between total energy stores and the rate of energy acquisition
 during germination under competition. The seed oil compositions of 391
 natural accessions of Arabidopsis thaliana, grown under common-garden
 conditions, were used to assess whether seed oil melting point within a
 species varied with germination temperature. In support of the adaptive
 explanation, long-term monthly spring and fall field temperatures of the
 accession collection sites significantly predicted their seed oil melting
 points. In addition, a genome-wide association study (GWAS) was performed
 to determine which genes were most likely responsible for the natural
 variation in seed oil melting point. The GWAS found a single highly
 significant association within the coding region of FAD2, which encodes a
 fatty acid desaturase central to the oil biosynthesis pathway. In a
 separate analysis of fifteen a priori oil synthesis candidate genes, two
 (FAD2 and FATB) were located near significant SNPs associated with seed
 oil melting point. These results comport with others’ molecular work
 showing that lines with alterations in these genes affect seed oil melting
 point as expected. Our results suggest natural selection has acted on a
 small number of loci to alter a quantitative trait in response to local
 environmental conditions.
description: TableS1Phenotypic, climatic, and geographic data for the Arabidopsis thaliana accessions used in this study.TableS2Seed oil melting points and box-cox transformed melting points for all replicates of the 391 Arabidopsis thaliana accessions.TableS3P-values and FDR-corrected values for the a priori candidate gene analysis.TableS4P-values and FDR-corrected values from GWAS based on analysis of boxcox-transformed melting points.TableS5Linkage disequilibrium between the two highly significant SNPs and all other SNPs within 1Mb up or downstream.TableS6P-values from GWAS with highly significant SNP on chromosome 3 (position=3860685 bp) as a covariate in the model.TableS7P-values from GWAS with highly significant SNP on chromosome 3 (position=3862256 bp) as a covariate in the model.TableS8Genes found within the 400kb haplotype block surrounding highly significant SNPs.TableS9Annotation information for all potential a posteriori candidate genes from the FAD2 haplotype block.
DOI: 10.5061/dryad.7h4j4
title: Data from: The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

description: The tropical Andes of South America, the world’s richest biodiversity
 hotspot, are home to many rapid radiations. While geological, climatic,
 and ecological processes collectively explain such radiations, their
 relative contributions are seldom examined within a single clade. We
 explore the contribution of these factors by applying a series of
 diversification models that incorporate mountain building, climate change,
 and trait evolution to the first dated phylogeny of Andean bellflowers
 (Campanulaceae: Lobelioideae). Our framework is novel for its direct
 incorporation of geological data on Andean uplift into a macroevolutionary
 model. We show that speciation and extinction are differentially
 influenced by abiotic factors: speciation rates rose concurrently with
 Andean elevation, while extinction rates decreased during global cooling.
 Pollination syndrome and fruit type, both biotic traits known to
 facilitate mutualisms, played an additional role in diversification. These
 abiotic and biotic factors resulted in one of the fastest radiations
 reported to date: the centropogonids, whose 550 species arose in the last
 5 Myr. Our study represents a significant advance in our understanding of
 plant evolution in Andean cloud forests. It further highlights the power
 of combining phylogenetic and Earth science models to explore the
 interplay of geology, climate, and ecology in generating the world’s
 biodiversity.
description: Trait codings for BiSSE
 analysesExcel file of trait
 codings for the four traits used in our BiSSE analyses (pollination
 syndrome, fruit type, Andean presence, elevation).Lagomarsino_et_al_TraitCodings_BiSSE.xlsxPlastid DNA alignmentPhylip file of final alignment used for phylogeny inference. See partition file, also included.Lagomarsino_et_al_Alignment.phyDNA alignment partitioning schemePartitioning scheme for plastid DNA alignmentLagomarsino_et_al_AlignmentPartitions.txtPaleoelevation of the AndesData points for model of paleoelevation of the Andes through time which was used in paleoenvironmental-dependency analyses.Lagomarsino_et_al_PastAndeanElevation.txt
DOI: 10.5061/dryad.n5r49
title: Data from: Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking

description: Phylogenetic tree inference is a critical component of many systematic and
 evolutionary studies. The majority of these studies are based on the
 two-step process of multiple sequence alignment followed by tree
 inference, despite persistent evidence that the alignment step can lead to
 biased results. Here we present a two-part study that first presents
 PaHMM-Tree, a novel neighbour joining-based method that estimates pairwise
 distances without assuming a single alignment. We then use simulations to
 benchmark its performance against a wide-range of other phylogenetic tree
 inference methods, including the first comparison of alignment-free
 distance-based methods against more conventional tree estimation methods.
 Our new method for calculating pairwise distances based on statistical
 alignment provides distance estimates that are as accurate as those
 obtained using standard methods based on the true alignment. Pairwise
 distance estimates based on the two-step process tend to be substantially
 less accurate. This improved performance carries through to tree
 inference, where PaHMM-Tree provides more accurate tree estimates than all
 of the pairwise distance methods assessed. For close to moderately
 divergent sequence data we find that the two-step methods using
 statistical inference, where information from all sequences is included in
 the estimation procedure, tend to perform better than PaHMM-Tree,
 particularly full statistical alignment, which simultaneously estimates
 both the tree and the alignment. For deep divergences we find the
 alignment step becomes so prone to error that our distance-based
 PaHMM-Tree outperforms all other methods of tree inference. Finally, we
 find that the accuracy of alignment-free methods tends to decline faster
 than standard two-step methods in the presence of alignment uncertainty,
 and identify no conditions where alignment-free methods are equal to or
 more accurate than standard phylogenetic methods even in the presence of
 substantial alignment error.
description: PaHMM-Tree supplementary
 materialSupplementary
 figuresPaHMM-Tree_supplementary_r1.docx
DOI: 10.5061/dryad.2sq1r
title: Data from: Resurrection of the island rule - human-driven extinctions have obscured a basic evolutionary pattern

description: Islands are or have been occupied by unusual species, such as dwarf
 proboscideans and giant rodents. The discussion of the classical, but
 controversial “island rule,” which states that mammalian body sizes
 converge on intermediate sizes on islands, has been stimulated by these
 unusual species. In this study, we use an unprecedented global data set of
 the distributions and body sizes of late-Quaternary mammal species and a
 novel analytical method to analyze body size evolution on islands. The
 analyses produced strong support for the island rule. Islands have
 suffered massive human-driven losses of species, and we found that the
 support for the island rule was substantially stronger when the many
 late-Quaternary extinct species were also considered (particularly, the
 tendency for dwarfing in large taxa). The decisive support for the island
 rule in this study confirms that evolution plays out markedly different on
 islands and that human impact may obscure even fundamental evolutionary
 patterns.
description: A database of the size
 of all extant or extinct mammals from the Holocene or Late
 PleistoceneAn excel-sheet with the
 sizes and island status of all mammalian species. A full description is
 found in the first worksheet entitled MetadataAdditional file
 1.xlsx
DOI: 10.5061/dryad.hf040
title: Data from: Effectiveness of ritonavir-boosted protease inhibitor monotherapy in clinical practice even with previous virological failures to protease inhibitor-based regimens

description: Background and objective: Significant controversy still exists about
 ritonavir-boosted protease inhibitor monotherapy (mtPI/rtv) as a
 simplification strategy that is used up to now to treat patients that have
 not experienced previous virological failure (VF) while on protease
 inhibitor (PI)-based regimens. We have evaluated the effectiveness of two
 mtPI/rtv regimens in an actual clinical practice setting, including
 patients that had experienced previous VF with PI-based regimens. Methods:
 This retrospective study analyzed 1060 HIV-infected patients with
 undetectable viremia that were switched to lopinavir/ritonavir or
 darunavir/ritonavir monotherapy. In cases in which the patient had
 previously experienced VF while on a PI-based regimen, the lack of major
 HIV protease resistance mutations to lopinavir or darunavir, respectively,
 was mandatory. The primary endpoint of this study was the percentage of
 participants with virological suppression after 96 weeks according to
 intention-to-treat analysis (non-complete/missing= failure). Results: A
 total of 1060 patients were analyzed, including 205 with previous VF while
 on PI-based regimens, 90 of whom were on complex therapies due to
 extensive resistance. The rates of treatment effectiveness
 (intention-to-treat analysis) and virological efficacy (on-treatment
 analysis) at week 96 were 79.3% (CI95, 76.8?81.8) and 91.5% (CI95,
 89.6-93.4), respectively. No relationships were found between VF and
 earlier VF while on PI-based regimens, the presence of major or minor
 protease resistance mutations, the previous time on viral suppression,
 CD4+ T-cell nadir, and HCV-coinfection. Genotypic resistance tests were
 available in 49 out of the 74 patients with VFs and only four patients
 presented new major protease resistance mutations. Conclusion: Switching
 to mtPI/rtv achieves sustained virological control in most patients, even
 in those with previous VF on PI-based regimens as long as no major
 resistance mutations are present for the administered drug.
description: mtPIrtv in Andalusian
 2-2-2016