cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.13074
title: Data from: Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

description: Plant architecture, phenology and yield components of cultivated plants
 have repeatedly been shaped by selection to meet human needs and
 adaptation to different environments. Here we assessed the genetic
 architecture of 24 correlated maize traits that interact during plant
 cycle. Overall, 336 lines were phenotyped in a network of 9 trials and
 genotyped with 50K single-nucleotide polymorphisms. Phenology was the main
 factor of differentiation between genetic groups. Then yield components
 distinguished dents from lower yielding genetic groups. However, most of
 trait variation occurred within group and we observed similar overall and
 within group correlations, suggesting a major effect of pleiotropy and/or
 linkage. We found 34 quantitative trait loci (QTLs) for individual traits
 and six for trait combinations corresponding to PCA coordinates. Among
 them, only five were pleiotropic. We found a cluster of QTLs in a 5 Mb
 region around Tb1 associated with tiller number, ear row number and the
 first PCA axis, the latter being positively correlated to flowering time
 and negatively correlated to yield. Kn1 and ZmNIP1 were candidate genes
 for tillering, ZCN8 for leaf number and Rubisco Activase 1 for kernel
 weight. Experimental repeatabilities, numbers of QTLs and proportion of
 explained variation were higher for traits related to plant development
 such as tillering, leaf number and flowering time, than for traits
 affected by growth such as yield components. This suggests a simpler
 genetic determinism with larger individual QTL effects for the first
 category.
description: Phenotypic
 dataphenotypic data (Lsmeans
 used for association analysis)pheno.txt.zipGenotypic data50 KSNP data used for association genetics, see Ganal et al. 2011 PLos One for method descriptiongeno.txt.zip
DOI: 10.5061/dryad.kf154
title: Data from: Historical colonization and dispersal limitation supplement climate and topography in shaping species richness of African lizards (Reptilia: Agaminae)

description: To what extent deep-time dispersal limitation shapes present-day
 biodiversity at broad spatial scales remains elusive. Here, we compiled a
 continental dataset on the distributions of African lizard species in the
 reptile subfamily Agaminae (a relatively young, Neogene radiation of
 agamid lizards which ancestors colonized Africa from the Arabian
 peninsula) and tested to what extent historical colonization and dispersal
 limitation (i.e. accessibility from areas of geographic origin) can
 explain present-day species richness relative to current climate,
 topography, and climate change since the late Miocene (~10 mya), the
 Pliocene (~3 mya), and the Last Glacial Maximum (LGM, 0.021 mya). Spatial
 and non-spatial multi-predictor regression models revealed that
 time-limited dispersal via arid corridors is a key predictor to explain
 macro-scale patterns of species richness. In addition, current
 precipitation seasonality, current temperature of the warmest month,
 paleo-temperature changes since the LGM and late Miocene, and topographic
 relief emerged as important drivers. These results suggest that deep-time
 dispersal constraints — in addition to climate and mountain building —
 strongly shape current species richness of Africa’s arid-adapted taxa.
 Such historical dispersal limitation might indicate that natural movement
 rates of species are too slow to respond to rates of ongoing and projected
 future climate and land use change.
description: Shapefiles_all_Agaminae_sppDistribution data (GIS shape files) of agamid lizards in Africa in two Projected Coordinate Systems (LAEA, WGS84). See readme file for further details.Agama_distribution_data_Africa.zip
DOI: 10.5061/dryad.31qg7
title: Data from: Cityscape genetics: structural vs. functional connectivity of an urban lizard population

description: Functional connectivity is essential for the long-term persistence of
 populations. However, many studies assess connectivity with a focus on
 structural connectivity only. Cityscapes, namely urban landscapes, are
 particularly dynamic and include numerous potential anthropogenic barriers
 to animal movements, such as roads, traffic or buildings. To assess and
 compare structural connectivity of habitats and functional connectivity of
 gene flow of an urban lizard, we here combined species distribution models
 (SDMs) with an individual-based landscape genetic optimization procedure.
 The most important environmental factors of the SDMs are structural
 diversity and substrate type, with high and medium levels of structural
 diversity as well as open and rocky/gravel substrates contributing most to
 structural connectivity. By contrast, water cover was the best model of
 all environmental factors following landscape genetic optimization. The
 river is thus a major barrier to gene flow, while of the typical
 anthropogenic factors only buildings showed an effect. Nonetheless, using
 SDMs as a basis for landscape genetic optimization provided the highest
 ranked model for functional connectivity. Optimizing SDMs in this way can
 provide a sound basis for models of gene flow of the cityscape, and
 elsewhere, while presence-only and presence–absence modelling approaches
 showed differences in performance. Additionally, interpretation of results
 based on SDM factor importance can be misleading, dictating more thorough
 analyses following optimization of SDMs. Such approaches can be adopted
 for management strategies, for example aiming to connect native common
 wall lizard populations or disconnect them from non-native introduced
 populations, which are currently spreading in many cities in Central
 Europe.
description: Landscape genetic input
 filesInput asci files of all
 environmental factors and PO- and PA-raw models for ResistanceGA. Also,
 PO- and PA-optim models included. Ordered by rank of landscape genetic
 optimization procedure.GenotypesCoordinatesCoordinates of all sampled individuals (223)Coordinates_resistanceGACoordinates of the 198 individuals included in landscape genetic analysisinput files SDMstif images of all environmental factors included in SDMs
DOI: 10.5061/dryad.bg2s4
title: Data from: Forbidden fruit: human settlement and abundant fruit create an ecological trap for an apex omnivore

description: Habitat choice is an evolutionary product of animals experiencing
 increased fitness when preferentially occupying high-quality habitat.
 However, an ecological trap (ET) can occur when an animal is presented
 with novel conditions and the animal's assessment of habitat quality
 is poorly matched to its resulting fitness. We tested for an ET for
 grizzly (brown) bears using demographic and movement data collected in an
 area with rich food resources and concentrated human settlement. We
 derived measures of habitat attractiveness from occurrence models of bear
 food resources and estimated demographic parameters using DNA
 mark–recapture information collected over 8 years (2006–2013). We then
 paired this information with grizzly bear mortality records to investigate
 kill and movement rates. Our results demonstrate that a valley high in
 both berry resources and human density was more attractive than
 surrounding areas, and bears occupying this region faced 17% lower
 apparent survival. Despite lower fitness, we detected a net flow of bears
 into the ET, which contributed to a study-wide population decline. This
 work highlights the presence and pervasiveness of an ET for an apex
 omnivore that lacks the evolutionary cues, under human-induced rapid
 ecological change, to assess trade-offs between food resources and
 human-caused mortality, which results in maladaptive habitat selection.
description: Data and Analysis
 Scripts for Ecological Trap PaperData and Analysis
 Scripts for Ecological Trap Paper. Including R projs to ensure clear
 documentation of analyses.Data_EcoTrap.zip
DOI: 10.5061/dryad.72tp3
title: Data from: Colour lightness of dragonfly assemblages across North America and Europe

description: Dark-coloured ectotherms absorb energy from the environment at higher
 rates than light-coloured ectotherms. The thermal melanism hypothesis
 (TMH) states that this physical mechanism links the colour lightness of
 the body surfaces of ectotherms to their thermal environment and hence to
 their geographical distribution. Studies on different insect taxa in
 Europe found support for this prediction of the TMH. However, whether
 these results hold also for other biogeographical regions remains unclear.
 Here, we quantify and map the colour lightness of dragonfly species in
 North America and directly compare our results to previously published
 findings for Europe. We estimated the colour lightness of 152 North
 American dragonfly species from published illustrations, compiled their
 distribution data from the literature and combined all these data with six
 biologically relevant environmental variables. We evaluated the importance
 of phylogenetic autocorrelation for the spatial variation of mean colour
 lightness of dragonfly assemblages (grid cells of approximately 50 km × 50
 km size) by repeating all analyses also for the phylogenetically predicted
 component of the colour lightness of species and the species-specific
 deviation from this prediction. We also accounted for spatial
 autocorrelation with autoregressive error models. All statistical
 approaches showed that dragonfly assemblages from both continents
 consistently tended to be darker coloured in regions with cold climates
 and lighter coloured in regions with warm climates. Regression slopes,
 however, were significantly less steep, and the amount of variance
 explained by environmental variables was lower for North America than for
 Europe. Our results highlight the importance of colour lightness for the
 distribution of dragonfly species, but they also indicate that
 idiosyncrasies of the continents modify the general pattern.
description: Assemblage-level data
 for North America and EuropeTwo files include data
 for North American and European dragonfly assemblages, separately. This
 data was used for most analysis and figures. An additional file includes
 the pooled data, which we used to compare the slopes of correlations of
 colour lightness against selected climate variables between the two
 continents. Variables are: mean colour lightness (meanRGB), the
 phylogenetic component of colour lightness (mean_A), the specific
 component of colour lightness (mean_E), 19 aggreagted BIOCLIM varaibles
 (bio1_mean to bio19_mean), mean altitude (alt_mean) and geographical
 coordinates (lng and lat).data_files_-_Pinkert_et_al_2016(ECOG-02578).zip
DOI: 10.5061/dryad.00db7
title: Data from: Sequential turnovers of sex chromosomes in African clawed frogs (Xenopus) suggest some genomic regions are good at sex determination

description: Sexual differentiation is fundamentally important for reproduction, yet
 the genetic triggers of this developmental process can vary, even between
 closely related species. Recent studies have uncovered, for example,
 variation in the genetic triggers for sexual differentiation within and
 between species of African clawed frogs (genus Xenopus). Here, we extend
 these discoveries by demonstrating that yet another sex determination
 system exists in Xenopus, specifically in the species Xenopus borealis.
 This system evolved recently in an ancestor of X. borealis that had the
 same sex determination system as X. laevis, a system which itself is newly
 evolved. Strikingly, the genomic region carrying the sex determination
 factor in X. borealis is homologous to that of therian mammals, including
 humans. Our results offer insights into how the genetic underpinnings of
 conserved phenotypes evolve, and suggest an important role for cooption of
 genetic building blocks with conserved developmental roles.
description: nexus_phylogeny_alignmentsSee the READMEnexus_sex_linked_genesSee README.ScriptsSee READMEDryad_READMEThis is the README for all of the files.BEAST_xmlSee the READMEBEAST_gene_treesSee the README
DOI: 10.5281/zenodo.18387684
title: Submission to REFSQ 2026 additional material
DOI: 10.5281/zenodo.18387683
title: Submission to REFSQ 2026 additional material
DOI: 10.5061/dryad.mg430
title: Data from: The bear circadian clock doesn't 'sleep' during winter dormancy

description: Background: Most biological functions are synchronized to the
 environmental light:dark cycle via a circadian timekeeping system. Bears
 exhibit shallow torpor combined with metabolic suppression during winter
 dormancy. We sought to confirm that free-running circadian rhythms of body
 temperature (Tb) and activity were expressed in torpid grizzly (brown)
 bears and that they were functionally responsive to environmental light.
 We also measured activity and ambient light exposures in denning wild
 bears to determine if rhythms were evident and what the photic conditions
 of their natural dens were. Lastly, we used cultured skin fibroblasts
 obtained from captive torpid bears to assess molecular clock operation in
 peripheral tissues. Circadian parameters were estimated using robust
 wavelet transforms and maximum entropy spectral analyses. Results: Captive
 grizzly bears housed in constant darkness during winter dormancy expressed
 circadian rhythms of activity and Tb. The rhythm period of juvenile bears
 was significantly shorter than that of adult bears. However, the period of
 activity rhythms in adult captive bears was virtually identical to that of
 adult wild denning bears as was the strength of the activity rhythms.
 Similar to what has been found in other mammals, a single light exposure
 during the bear’s active period delayed subsequent activity onsets whereas
 these were advanced when light was applied during the bear’s inactive
 period. Lastly, in vitro studies confirmed the expression of molecular
 circadian rhythms with a period comparable to the bear’s own behavioral
 rhythms. Conclusions: Based on these findings we conclude that the
 circadian system is functional in torpid bears and their peripheral
 tissues even when housed in constant darkness, is responsive to
 phase-shifting effects of light, and therefore, is a normal facet of
 torpid bear physiology.
description: FronZool2016_FINZ-D-16-00043R2xlsx and csv files containing bear actigraphy and light data (lux) to accompany manuscript. Also included are body temperature data.
DOI: 10.34810/data1283
title: Partitura i enregistrament de "Sonata para clarines" Joaquim Laposaria Alsina (1778-1839) [fray Joaquín de Jesús María y José]

description: Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical, aquest dataset conté dos arxius: 
&lt;br&gt; Transcripció del manuscrit original de Joaquim Laposaria
Alsina 
&lt;br&gt; Enregistrament de la peça interpretada per: 
&lt;br&gt;- Javier Artigas, orgue. Orgue històric de l'església de la Asunción de
Cardenete, construït el 1767
DOI: 10.5061/dryad.g3pj8
title: Data from: Click or skip: the role of experience in easy-click checking decisions

description: New websites and smartphone applications provide easy-click checking
 opportunities that can help consumers in many domains. However, this
 technology is not always used effectively. For example, many consumers
 skip checking “Terms and Conditions” links even when a quick evaluation of
 the terms can save money, but check their smartphone while driving even
 thought this behavior is illegal and dangerous. Four laboratory
 experiments clarify the significance of one contributor to such
 contradictory deviations from effective checking. Studies 1, 2, and 3 show
 that, like basic decisions from experience, checking decisions reflect
 underweighting of rare events, which in turn is a sufficient condition for
 the coexistence of insufficient and too much checking. Insufficient
 checking emerges when most checking efforts impair performance even if
 checking is effective on average. Too much checking emerges when most
 checking clicks are rewarding even if checking is counterproductive on
 average. This pattern can be captured with a model that assumes reliance
 on small samples of past checking decision experiences. Study 4 shows that
 when the goal is to increase checking, interventions which increase the
 probability that checking leads to the best possible outcome can be far
 more effective than efforts to reduce the cost of checking.
description: All
 Data_SubmitionAll the data appearing
 in the paper "Click or Skip: The Role Of Experience In Easy-Click
 Checking Decisions"
DOI: 10.5061/dryad.1g626
title: Data from: Postnatal ontogeny and the evolution of macrostomy in snakes

description: Macrostomy is the anatomical feature present in macrostomatan snakes that
 permits the ingestion of entire prey with high cross-sectional area. It
 depends on several anatomical traits in the skeleton and soft tissues, of
 which the elongation of gnathic complex and backward rotation of the
 quadrate represent crucial skeletal requirements. Here, the relevance of
 postnatal development of these skull structures and their relationship
 with macrohabitat and diet are explored. Contrary to the condition present
 in lizards and basal snakes that occupy underground macrohabitats,
 elements of the gnathic complex of most macrostomatan snakes that exploit
 surface macrohabitats display conspicuous elongation during postnatal
 growth, relative to the rest of the skull, as well as further backward
 rotation of the quadrate bone. Remarkably, several clades of small
 cryptozoic macrostomatans reverse these postnatal transformations and
 return to a diet based on prey with low cross-sectional area such as
 annelids, insects or elongated vertebrates, thus resembling the condition
 present in underground basal snakes. Dietary ontogenetic shift observed in
 most macrostomatan snakes is directly linked with this ontogenetic
 trajectory, indicating that this shift is acquired progressively as the
 gnathic complex elongates and the quadrate rotates backward during
 postnatal ontogeny. The numerous independent events of reversion in the
 gnathic complex and prey type choice observed in underground
 macrostomatans and the presence of skeletal requirements for macrostomy in
 extinct non-macrostomatan species reinforce the possibility that basal
 snakes represent underground survivors of clades that had the skeletal
 requirements for macrostomy. Taken together, the data presented here
 suggest that macrostomy has been shaped during multiple episodes of
 occupation of underground and surface macrohabitats throughout the
 evolution of snakes.
description: Electronic supplementary
 material S2Electronic supplementary
 material S1
DOI: 10.5061/dryad.qk58h
title: Data from: Rarefaction and extrapolation: making fair comparison of abundance-sensitive phylogenetic diversity among multiple assemblages

description: Measures of phylogenetic diversity are basic tools in many studies of
 systematic biology. Faith’s PD (sum of branch lengths of a phylogenetic
 tree connecting all focal species) is the most widely used phylogenetic
 measure. Like species richness, Faith’s PD based on sampling data is
 highly dependent on sample size and sample completeness. The sample-size-
 and sample-coverage-based integration of rarefaction and extrapolation of
 Faith’s PD was recently developed to make fair comparison across multiple
 assemblages. However, species abundances are not considered in Faith’s PD.
 Based on the framework of Hill numbers, Faith’s PD was generalized to a
 class of phylogenetic diversity measures that incorporates species
 abundances. In this article, we develop both theoretical formulae and
 analytic estimators for seamless rarefaction and extrapolation for this
 class of abundance-sensitive phylogenetic measures, which includes simple
 transformations of phylogenetic entropy and of quadratic entropy. This
 work generalizes the previous rarefaction/extrapolation model of Faith’s
 PD to incorporate species abundance, and also extends the previous
 rarefaction/extrapolation model of Hill numbers to include phylogenetic
 differences among species. Thus a unified approach to assessing and
 comparing species/taxonomic diversity and phylogenetic diversity can be
 established. A bootstrap method is suggested for constructing confidence
 intervals around the phylogenetic diversity, facilitating the comparison
 of multiple assemblages. Our formulation and estimators can be extended to
 incidence data collected from multiple sampling units. We also illustrate
 the formulae and estimators using bacterial sequence data from the human
 distal esophagus and phyllostomid bat data from three habitats.
description: Appendix A Final
 (Replication Principle)Replication principle
 for species diversity and phylogenetic diversityAppendix B Final
 (Extrapolation)Extrapolation formulas
 for phylogenetic diversityAppendix C Final
 (Simulation Studies)Using simulation to test
 the proposed methodsAppendix D Final
 (BacterialData)The 16S rRNA sequence
 bacterial biota data and phylogenetic tree from the human distal
 esophagusAppendix E Final
 (BatData)Rarefaction and
 extrapolation analysis for bat dataAppendix F Final
 (Comparison)Comparison of
 rarefaction/extrapolation sampling curves for species diversity and
 phylogenetic diversityAppendix G Final
 (reference points)Relationship between the
 phylogenetic diversities of two temporal reference
 pointsAppendix H Final
 (IncidenceData)Rarefaction and
 extrapolation of abundance-sensitive phylogenetic diversity based on
 incidence data
DOI: 10.5061/dryad.n36st
title: Data from: DNA barcodes of the native ray-finned fishes in Taiwan

description: Species identification based on the DNA sequence of a fragment of the
 cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome, DNA
 barcoding, is widely applied to assist in sustainable exploitation of fish
 resources and the protection of fish biodiversity. The aim of this study
 was to establish a reliable barcoding reference database of the native
 ray-finned fishes in Taiwan. A total of 2,993 individuals, belonging to
 1,245 species within 637 genera, 184 families, and 29 orders of ray-finned
 fishes and representing approximately 40% of the recorded ray-finned
 fishes in Taiwan, were PCR amplified at the barcode region and
 bidirectionally sequenced. The mean length of the 2,993 barcodes is 549
 bp. Mean congeneric K2P distance (15.24%) is approximately 10-fold higher
 than the mean conspecific one (1.51%), but roughly 1.4-fold less than the
 mean genetic distance between families (20.80%). The Barcode Index Number
 (BIN) discordance report shows that 2,993 specimens represent 1,275 BINs
 and, among them, 86 BINs are singletons, 570 BINs are taxonomically
 concordant, and the other 619 BINs are taxonomically discordant. Barcode
 gap analysis also revealed that more than 90% of the collected fishes in
 this study can be discriminated by DNA barcoding. Overall, the barcoding
 reference database established by this study reveals the need for
 taxonomic revisions and voucher specimen rechecks, in addition to
 assisting in the management of Taiwan's fish resources and diversity.
description: MER
 alignthe fasta file of the
 aligned 2993 DNA barcoding sequencesBOLDTreeTaxon ID tree in the newick tree format
DOI: 10.15468/dl.pf6zqw
title: Occurrence Download

description: A dataset containing 882836 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is FRA.1.5.3_1",
 "PublishingOrg is 1928bdf0-f5d2-11dc-8c12-b8a03c50a862"
 ]
}

 The dataset includes 882836 records from 702 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001449-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.